/*
* 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.control.admin;
import java.io.FileInputStream;
import java.io.IOException;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.*;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import org.akaza.openclinica.bean.admin.CRFBean;
import org.akaza.openclinica.bean.admin.NewCRFBean;
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.core.Utils;
import org.akaza.openclinica.bean.login.UserAccountBean;
import org.akaza.openclinica.bean.oid.MeasurementUnitOidGenerator;
import org.akaza.openclinica.bean.submit.CRFVersionBean;
import org.akaza.openclinica.bean.submit.ItemBean;
import org.akaza.openclinica.bean.submit.ItemFormMetadataBean;
import org.akaza.openclinica.bean.submit.ItemGroupBean;
import org.akaza.openclinica.bean.submit.ResponseSetBean;
import org.akaza.openclinica.control.form.Validator;
import org.akaza.openclinica.core.form.StringUtil;
import org.akaza.openclinica.dao.admin.CRFDAO;
import org.akaza.openclinica.dao.core.CoreResources;
import org.akaza.openclinica.dao.hibernate.MeasurementUnitDao;
import org.akaza.openclinica.dao.submit.CRFVersionDAO;
import org.akaza.openclinica.dao.submit.ItemDAO;
import org.akaza.openclinica.dao.submit.ItemDataDAO;
import org.akaza.openclinica.dao.submit.ItemGroupDAO;
import org.akaza.openclinica.exception.CRFReadingException;
import org.akaza.openclinica.logic.score.ScoreValidator;
import org.akaza.openclinica.web.SQLInitServlet;
import org.apache.poi.hssf.usermodel.HSSFCell;
import org.apache.poi.hssf.usermodel.HSSFSheet;
import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* <P>
* Returns multiple types of things based on the parsing; returns html table
* returns data objects as SQL strings.
* <P>
* The most important method here is the toNIB() method, which returns the
* NewInstrumentBean which in turn creates a new instrument version in the
* database.
*
*
* @author thickerson with help from Brian Gilman @ the Whitehead Institute
* modified by jxu
* @version CVS: $Id: SpreadSheetTable.java,v 1.28 2006/09/01 00:37:19 jxu Exp $
*/
public class SpreadSheetTableClassic implements SpreadSheetTable {// extends
// SpreadSheetTable
// {
private POIFSFileSystem fs = null;
private UserAccountBean ub = null;
private String versionName = null;
private int crfId = 0;
private String crfName = "";
private String versionIdString = "";
private Locale locale;
private final int studyId;
private Set<String> existingUnits = new TreeSet<String>();
private Set<String> existingOIDs = new TreeSet<String>();
private MeasurementUnitDao measurementUnitDao = new MeasurementUnitDao();
// the default; all crf ids should be > 0, tbh 8-29 :-)
protected final Logger logger = LoggerFactory.getLogger(getClass().getName());
public SpreadSheetTableClassic(FileInputStream parseStream, UserAccountBean ub, String versionName, Locale locale, int studyId) throws IOException {
// super();
this.fs = new POIFSFileSystem(parseStream);
this.ub = ub;
this.versionName = versionName;
this.locale = locale;
this.studyId = studyId;
}
public void setCrfId(int id) {
this.crfId = id;
}
public int getCrfId() {
return this.crfId;
}
public NewCRFBean toNewCRF(javax.sql.DataSource ds, ResourceBundle resPageMsg) throws IOException, CRFReadingException {
String dbName = SQLInitServlet.getDBName();
NewCRFBean ncrf = new NewCRFBean(ds, crfId);
ncrf.setCrfId(crfId);// set crf id
StringBuffer buf = new StringBuffer();
HSSFWorkbook wb = new HSSFWorkbook(fs);
int numSheets = wb.getNumberOfSheets();
ArrayList queries = new ArrayList();
ArrayList errors = new ArrayList();
ArrayList repeats = new ArrayList();
HashMap tableNames = new HashMap();
HashMap items = new HashMap();
String pVersion = "";
String pVerDesc = "";
int parentId = 0;
int dataTypeId = 5;// default is ST(String) type
HashMap itemCheck = ncrf.getItemNames();
HashMap GroupCheck = ncrf.getItemGroupNames();
HashMap openQueries = new LinkedHashMap();
HashMap backupItemQueries = new LinkedHashMap();// save all the item
// queries if
// deleting item happens
ArrayList secNames = new ArrayList(); // check for dupes, also
// YW 1-30-2008
HashMap<String, String> allItems = new HashMap<String, String>();
ArrayList<String> itemGroupOids = new ArrayList<String>();
ArrayList<String> itemOids = new ArrayList<String>();
CRFDAO cdao = new CRFDAO(ds);
CRFBean crf = (CRFBean) cdao.findByPK(crfId);
ItemDataDAO iddao = new ItemDataDAO(ds);
ItemDAO idao = new ItemDAO(ds);
CRFVersionDAO cvdao = new CRFVersionDAO(ds);
ItemGroupDAO itemGroupDao = new ItemGroupDAO(ds);
int validSheetNum = 0;
for (int j = 0; j < numSheets; j++) {
HSSFSheet sheet = wb.getSheetAt(j);// sheetIndex);
String sheetName = wb.getSheetName(j);
if (sheetName.equalsIgnoreCase("CRF") || sheetName.equalsIgnoreCase("Sections") || sheetName.equalsIgnoreCase("Items")) {
validSheetNum++;
}
}
if (validSheetNum != 3) {
// errors.add("The excel spreadsheet doesn't have required valid
// worksheets. Please check whether it contains" +
// " sheets of CRF, Sections and Items.");
errors.add(resPageMsg.getString("excel_not_have_valid_worksheet"));
}
// check to see if questions are referencing a valid section name, tbh
// 7/30
for (int j = 0; j < numSheets; j++) {
HSSFSheet sheet = wb.getSheetAt(j);// sheetIndex);
String sheetName = wb.getSheetName(j);
if (sheetName.equalsIgnoreCase("Instructions")) {
// totally ignore instructions
} else {
/*
* current strategem: build out the queries by hand and revisit
* this as part of the data loading module. We begin to check
* for errors here and look for blank cells where there should
* be data, tbh, 7/28
*/
int numRows = sheet.getPhysicalNumberOfRows();
int lastNumRow = sheet.getLastRowNum();
// logger.info("PhysicalNumberOfRows" +
// sheet.getPhysicalNumberOfRows());
logger.info("PhysicalNumberOfRows" + sheet.getPhysicalNumberOfRows());
// logger.info("LastRowNum()" + sheet.getLastRowNum());
String secName = "";
String page = "";
ArrayList resNames = new ArrayList();// records all the
// response_labels
HashMap htmlErrors = new HashMap();
// the above two need to persist across mult. queries,
// and they should be created FIRST anyway, since instrument is
// first
// also need to add to VERSIONING_MAP, tbh, 6-6-3
// try to count how many blank rows, if 5 concective blank rows
// found, stop reading
int blankRowCount = 0;
if (sheetName.equalsIgnoreCase("Items")) {
logger.info("read an item in sheet" + sheetName);
Map labelWithType = new HashMap<String, String>();
// let's insert the default group first
ItemGroupBean defaultGroup = new ItemGroupBean();
defaultGroup.setName("Ungrouped");
defaultGroup.setCrfId(crfId);
defaultGroup.setStatus(Status.AVAILABLE);
// Create oid for Item Group
String defaultGroupOid = itemGroupDao.getValidOid(defaultGroup, crfName, defaultGroup.getName(), itemGroupOids);
itemGroupOids.add(defaultGroupOid);
String defaultSql = "";
if (dbName.equals("oracle")) {
defaultSql =
"INSERT INTO ITEM_GROUP ( " + "name, crf_id, status_id, date_created ,owner_id,oc_oid)" + "VALUES ('" + defaultGroup.getName()
+ "', " + defaultGroup.getCrfId() + "," + defaultGroup.getStatus().getId() + "," + "sysdate," + ub.getId() + ",'"
+ defaultGroupOid + "')";
} else {
defaultSql =
"INSERT INTO ITEM_GROUP ( " + "name, crf_id, status_id, date_created ,owner_id,oc_oid)" + "VALUES ('" + defaultGroup.getName()
+ "', " + defaultGroup.getCrfId() + "," + defaultGroup.getStatus().getId() + "," + "now()," + ub.getId() + ",'"
+ defaultGroupOid + "')";
}
if (!GroupCheck.containsKey("Ungrouped")) {
queries.add(defaultSql);
}
//Adding itemnames for further use
HashMap itemNames = new HashMap();
for (int k = 1; k < numRows; k++) {
HSSFCell cell = sheet.getRow(k).getCell((short) 0);
String itemName = getValue(cell);
itemName = itemName.replaceAll("<[^>]*>", "");
itemNames.put(k, itemName);
}
for (int k = 1; k < numRows; k++) {
// logger.info("hit row "+k);
if (blankRowCount == 5) {
logger.info("hit end of the row ");
break;
}
if (sheet.getRow(k) == null) {
blankRowCount++;
continue;
}
HSSFCell cell = sheet.getRow(k).getCell((short) 0);
String itemName = getValue(cell);
itemName = itemName.replaceAll("<[^>]*>", "");
// regexp to make sure it is all word characters, '\w+' in regexp terms
if (!Utils.isMatchingRegexp(itemName, "\\w+")) {
// different item error to go here
errors.add(resPageMsg.getString("item_name_column") + " " + resPageMsg.getString("was_invalid_at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("you_can_only_use_letters_or_numbers"));
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("INVALID_FIELD"));
}
if (StringUtil.isBlank(itemName)) {
// errors.add("The ITEM_NAME column was blank at row
// " + k + ", Items worksheet.");
// htmlErrors.put(j + "," + k + ",0", "REQUIRED
// FIELD");
errors.add(resPageMsg.getString("item_name_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("required_field"));
}
if (itemName != null && itemName.length() > 255) {
errors.add(resPageMsg.getString("item_name_length_error"));
}
if (repeats.contains(itemName)) {
// errors.add("A duplicate ITEM_NAME of " + itemName
// + " was detected at row " + k
// + ", Items worksheet.");
// htmlErrors.put(j + "," + k + ",0", "DUPLICATE
// FIELD");
errors.add(resPageMsg.getString("duplicate") + " " + resPageMsg.getString("item_name_column") + " " + itemName + " "
+ resPageMsg.getString("was_detected_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("required_field"));
} else if (itemName.length() > 0) {
allItems.put(itemName, "Ungrouped");
}
repeats.add(itemName);
cell = sheet.getRow(k).getCell((short) 1);
String descLabel = getValue(cell);
descLabel = descLabel.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(descLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DESCRIPTION_LABEL_column") + " "
+ resPageMsg.getString("was_blank_at_row") + " " + k + "," + resPageMsg.getString("items_worksheet") + ".");
// errors.add("The DESCRIPTION_LABEL column was
// blank at row " + k + "," +
// resPageMsg.getString("items_worksheet") +".");
htmlErrors.put(j + "," + k + ",1", resPageMsg.getString("required_field"));
}
if (descLabel != null && descLabel.length() > 4000) {
errors.add(resPageMsg.getString("item_desc_length_error"));
}
cell = sheet.getRow(k).getCell((short) 2);
String leftItemText = getValue(cell);
if (leftItemText != null && leftItemText.length() > 4000) {
errors.add(resPageMsg.getString("left_item_length_error"));
}
// Commented out to resolve issue-2413
// if (StringUtil.isBlank(leftItemText)) {
// errors.add(resPageMsg.getString("the") + " " +
// resPageMsg.getString("LEFT_ITEM_TEXT_column") + " "
// + resPageMsg.getString("was_blank_at_row") + k + ","
// + resPageMsg.getString("items_worksheet") + ".");
// htmlErrors.put(j + "," + k + ",2",
// resPageMsg.getString("required_field"));
// }
cell = sheet.getRow(k).getCell((short) 3);
String unit = getValue(cell).trim();
if (unit != null && unit.length() > 0) {
String muSql = "";
if (this.existingUnits.size() > 0) {
} else {
this.existingUnits = this.measurementUnitDao.findAllNamesInUpperCase();
if (this.existingUnits == null) {
this.existingUnits = new TreeSet<String>();
}
}
if (this.existingOIDs.size() > 0) {
} else {
this.existingOIDs = this.measurementUnitDao.findAllOIDs();
if (this.existingOIDs == null) {
this.existingOIDs = new TreeSet<String>();
}
}
if (this.existingUnits.contains(unit.toUpperCase())) {
this.logger.error("unit=" + unit + " existed.");
} else {
String oid = "";
try {
oid = new MeasurementUnitOidGenerator().generateOidNoValidation(unit);
} catch (Exception e) {
throw new RuntimeException("CANNOT GENERATE OID");
}
if(this.existingOIDs.contains(oid)) {
if(oid.length()>40) {
oid = oid.substring(0, 35);
}
oid = new MeasurementUnitOidGenerator().randomizeOid(oid);
}
this.existingOIDs.add(oid);
this.existingUnits.add(unit.toUpperCase());
muSql = this.getMUInsertSql(oid, unit, ub.getId(), dbName);
queries.add(muSql);
}
}
cell = sheet.getRow(k).getCell((short) 4);
String rightItemText = getValue(cell);
if (rightItemText != null && rightItemText.length() > 2000) {
errors.add(resPageMsg.getString("right_item_length_error"));
}
cell = sheet.getRow(k).getCell((short) 5);
if (cell != null) {
secName = getValue(cell);
secName = secName.replaceAll("<[^>]*>", "");
}
if (secName != null && secName.length() > 2000) {
errors.add(resPageMsg.getString("section_label_length_error"));
}
if (!secNames.contains(secName)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column") + " "
+ resPageMsg.getString("not_valid_section_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". "
+ resPageMsg.getString("check_to_see_that_there_is_valid_LABEL"));
htmlErrors.put(j + "," + k + ",5", resPageMsg.getString("NOT_A_VALID_LABEL"));
}
cell = sheet.getRow(k).getCell((short) 6);
String header = getValue(cell);
if (header != null && header.length() > 2000) {
errors.add(resPageMsg.getString("item_header_length_error"));
}
cell = sheet.getRow(k).getCell((short) 7);
String subHeader = getValue(cell);
if (subHeader != null && subHeader.length() > 240) {
errors.add(resPageMsg.getString("item_subheader_length_error"));
}
cell = sheet.getRow(k).getCell((short) 8);
String parentItem = getValue(cell);
parentItem = parentItem.replaceAll("<[^>]*>", "");
// Checking for a valid paren item name
if(!StringUtil.isBlank(parentItem)){
if(!itemNames.containsValue(parentItem)){
errors.add("the Parent item specified on row "+k+" does not exist in the CRF template. Please update the value. ");
}
}
// BWP>>Prevent parent names that equal the Item names
if (itemName != null && itemName.equalsIgnoreCase(parentItem)) {
parentItem = "";
}
cell = sheet.getRow(k).getCell((short) 9);
int columnNum = 0;
String column = getValue(cell);
if (!StringUtil.isBlank(column)) {
try {
columnNum = Integer.parseInt(column);
} catch (NumberFormatException ne) {
columnNum = 0;
}
}
cell = sheet.getRow(k).getCell((short) 10);
if (cell != null) {
page = getValue(cell);
}
cell = sheet.getRow(k).getCell((short) 11);
String questionNum = getValue(cell);
cell = sheet.getRow(k).getCell((short) 12);
String responseType = getValue(cell);
int responseTypeId = 1;
if (StringUtil.isBlank(responseType)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_TYPE_column") + " "
+ resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",12", resPageMsg.getString("required_field"));
} else {
if (!ResponseType.findByName(responseType.toLowerCase())) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_TYPE_column") + " "
+ resPageMsg.getString("was_invalid_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",12", resPageMsg.getString("INVALID_FIELD"));
} else {
responseTypeId = ResponseType.getByName(responseType.toLowerCase()).getId();
}
}
cell = sheet.getRow(k).getCell((short) 13);
String responseLabel = getValue(cell);
// responseLabel = responseLabel.replaceAll("<[^>]*>",
// "");
if (StringUtil.isBlank(responseLabel) && responseTypeId != ResponseType.TEXT.getId()
&& responseTypeId != ResponseType.TEXTAREA.getId()) {
// << tbh #4180
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_LABEL_column") + " "
+ resPageMsg.getString("was_blank_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",13", resPageMsg.getString("required_field"));
} else if ("file".equalsIgnoreCase(responseType) && !"file".equalsIgnoreCase(responseLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_LABEL_column") + " "
+ resPageMsg.getString("should_be_file") + resPageMsg.getString("at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",13", resPageMsg.getString("should_be_file"));
}
cell = sheet.getRow(k).getCell((short) 14);
String resOptions = getValue(cell);
// resOptions = resOptions.replaceAll("<[^>]*>", "");
if (responseLabel.equalsIgnoreCase("text") || responseLabel.equalsIgnoreCase("textarea")) {
resOptions = "text";
}
if ("file".equalsIgnoreCase(responseType)) {
resOptions = "file";
}
// YW 2-5-2008 << set default resOptions for calculation
// and group-calculation type
// if(responseTypeId==8 || responseTypeId==9) {
// resOptions = resOptions.length()>0 ? resOptions :
// "can not calculate";
// }
// YW >>
int numberOfOptions = 0;
if (!resNames.contains(responseLabel) && StringUtil.isBlank(resOptions) && responseTypeId != ResponseType.TEXT.getId()
&& responseTypeId != ResponseType.TEXTAREA.getId()) {
// << tbh #4180
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_OPTIONS_TEXT_column")
+ resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",14", resPageMsg.getString("required_field"));
}
if (!resNames.contains(responseLabel) && !StringUtil.isBlank(resOptions)) {
// YW 1-29-2008 << only one option for "calculation"
// type and "group-calculation" type
// but do we really need this variable these two
// types?
// actually, responseTypeId=9 is not necessary for
// old template
if (responseTypeId == 8 || responseTypeId == 9) {
numberOfOptions = 1;
// YW >>
} else {
// String[] resArray = resOptions.split(",");
String text1 = resOptions.replaceAll("\\\\,", "##");
String[] resArray = text1.split(",");
numberOfOptions = resArray.length;
}
}
cell = sheet.getRow(k).getCell((short) 15);
String resValues = getValue(cell);
String value1 = resValues.replaceAll("\\\\,", "##");
String[] resValArray = value1.split(",");
if (responseLabel.equalsIgnoreCase("text") || responseLabel.equalsIgnoreCase("textarea")) {
resValues = "text";
}
if ("file".equalsIgnoreCase(responseType)) {
resValues = "file";
}
if (!resNames.contains(responseLabel) && StringUtil.isBlank(resValues) && responseTypeId != ResponseType.TEXT.getId()
&& responseTypeId != ResponseType.TEXTAREA.getId()) {
// << tbh, #4180, add textarea too?
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " "
+ resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("required_field"));
}
// YW 1-25-2008 << validate scoring expression
if (responseTypeId == 8 || responseTypeId == 9) {
// right now, func is not required; but if there is
// func, it must be correctly spelled
if (resValues.contains(":")) {
String[] s = resValues.split(":");
if (!"func".equalsIgnoreCase(s[0].trim())) {
errors.add(resPageMsg.getString("expression_not_start_with_func_at") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("INVALID_FIELD"));
}
}
String exp = resValues;
// make both \\, and , works for functions
exp = exp.replace("\\\\,", "##");
exp = exp.replace("##", ",");
exp = exp.replace(",", "\\\\,");
resValues = exp;
if (exp.startsWith("func:")) {
exp = exp.substring(5).trim();
}
exp = exp.replace("\\\\,", "##");
StringBuffer err = new StringBuffer();
ArrayList<String> variables = new ArrayList<String>();
ScoreValidator scoreValidator = new ScoreValidator(locale);
if (!scoreValidator.isValidExpression(exp, err, variables)) {
errors.add(resPageMsg.getString("expression_invalid_at") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ": "
+ err);
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("INVALID_FIELD"));
}
String group = "Ungrouped";
for (String v : variables) {
if (!allItems.containsKey(v)) {
errors.add(resPageMsg.getString("item") + v + resPageMsg.getString("must_listed_before_item") + itemName
+ resPageMsg.getString("item_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("INVALID_FIELD"));
}
}
} else if (numberOfOptions > 0) {
// YW >>
if (resValArray.length != numberOfOptions) {
errors.add(resPageMsg.getString("incomplete_option_value_pair") + " " + resPageMsg.getString("RESPONSE_OPTIONS_column") + " "
+ resPageMsg.getString("and") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " " + resPageMsg.getString("at_row") + k
+ " " + resPageMsg.getString("items_worksheet") + "; " + resPageMsg.getString("perhaps_missing_comma"));
htmlErrors.put(j + ", " + k + ", 14", resPageMsg.getString("number_option_not_match"));
htmlErrors.put(j + ", " + k + ", 15", resPageMsg.getString("number_value_not_match"));
}
}
cell = sheet.getRow(k).getCell((short) 16);
String dataType = getValue(cell);
dataType = dataType.replaceAll("<[^>]*>", "");
String dataTypeIdString = "1";
if (StringUtil.isBlank(dataType)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " "
+ resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet"));
htmlErrors.put(j + ", " + k + ", 16", resPageMsg.getString("required_field"));
} else {
if (!ItemDataType.findByName(dataType.toLowerCase())) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " "
+ resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 16", resPageMsg.getString("INVALID_FIELD"));
} else {
if ("file".equalsIgnoreCase(responseType) && !"FILE".equalsIgnoreCase(dataType)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " "
+ resPageMsg.getString("should_be_file") + " "+resPageMsg.getString("at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 16", resPageMsg.getString("should_be_file"));
}
// dataTypeId =
// (ItemDataType.getByName(dataType)).getId();
dataTypeIdString = "(SELECT ITEM_DATA_TYPE_ID From ITEM_DATA_TYPE Where CODE='" + dataType.toUpperCase() + "')";
}
}
if (responseTypeId == 3 || responseTypeId == 5 || responseTypeId == 6 || responseTypeId == 7) {
// make sure same responseLabels have same datatype
if (labelWithType.containsKey(responseLabel)) {
logger.debug("in label=" + responseLabel);
if (!dataType.equalsIgnoreCase(labelWithType.get(responseLabel).toString())) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " "
+ resPageMsg.getString("does_not_match_the_item_data_type_with_the_same_response_label") + " " + k + ", "
+ resPageMsg.getString("items_worksheet"));
htmlErrors.put(j + "," + k + ",16", resPageMsg.getString("INVALID_FIELD"));
}
} else {
labelWithType.put(responseLabel, dataType);
// make sure response values matching datatype
if (resValArray.length > 0) {
boolean wrongType = false;
if ("int".equalsIgnoreCase(dataType)) {
for (String s : resValArray) {
String st = s != null && s.length() > 0 ? s.trim() : "";
if (st.length() > 0) {
try {
Integer I = Integer.parseInt(s.trim());
// eg, s=2.3 => I=2,
// but 2.3 is not integer
if (!I.toString().equals(s.trim())) {
wrongType = true;
}
} catch (Exception e) {
wrongType = true;
}
}
}
if (wrongType) {
wrongType = false;
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " "
+ resPageMsg.getString("should_be_integer") + " " + resPageMsg.getString("at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 15", resPageMsg.getString("should_be_integer"));
}
} else if ("real".equalsIgnoreCase(dataType)) {
for (String s : resValArray) {
String st = s != null && s.length() > 0 ? s.trim() : "";
if (st.length() > 0) {
try {
Double I = Double.parseDouble(s.trim());
} catch (Exception e) {
wrongType = true;
}
}
}
if (wrongType) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " "
+ resPageMsg.getString("should_be_real") + " " + resPageMsg.getString("at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 15", resPageMsg.getString("should_be_real"));
}
}
}
}
}
cell = sheet.getRow(k).getCell((short) 17);
String regexp = getValue(cell);
String regexp1 = "";
if (!StringUtil.isBlank(regexp)) {
// parse the string and get reg exp eg. regexp:
// /[0-9]*/
regexp1 = regexp.trim();
if (regexp1.startsWith("regexp:")) {
String finalRegexp = regexp1.substring(7).trim();
if (finalRegexp.contains("\\\\")) {
// \\ in the regular expression it should
// not be allowed
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + " "
+ resPageMsg.getString("has_an_invalid_regular_expression_at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("regular_expression_contained") + " '\\\\', "
+ resPageMsg.getString("it_should_only_contain_one") + "'\\'. ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
} else {
if (finalRegexp.startsWith("/") && finalRegexp.endsWith("/")) {
finalRegexp = finalRegexp.substring(1, finalRegexp.length() - 1);
try {
Pattern p = Pattern.compile(finalRegexp);
// YW 11-21-2007 << add another \ if
// there is \ in regexp
char[] chars = regexp1.toCharArray();
regexp1 = "";
for (char c : chars) {
if (c == '\\' && !dbName.equals("oracle")) {
regexp1 += c + "\\";
} else {
regexp1 += c;
}
}
// YW >>
} catch (PatternSyntaxException pse) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column")
+ resPageMsg.getString("has_an_invalid_regular_expression_at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("Example:") + " regexp: /[0-9]*/ ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
} else {
// errors.add("The VALIDATION column has
// an invalid regular expression at row
// " + k
// + ", Items worksheet. Example:
// regexp: /[0-9]*/ ");
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + " "
+ resPageMsg.getString("has_an_invalid_regular_expression_at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("Example") + " regexp: /[0-9]*/ ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
}
} else if (regexp1.startsWith("func:")) {
boolean isProperFunction = false;
try {
Validator.processCRFValidationFunction(regexp1);
isProperFunction = true;
} catch (Exception e) {
errors.add(e.getMessage() + ", " + resPageMsg.getString("at_row") + " " + k + ", "
+ resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
} else {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + " "
+ resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
}
cell = sheet.getRow(k).getCell((short) 18);
String regexpError = getValue(cell);
regexpError = regexpError.replaceAll("<[^>]*>", "");
if (!StringUtil.isBlank(regexp) && StringUtil.isBlank(regexpError)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_ERROR_MESSAGE_column")
+ resPageMsg.getString("was_blank_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ". "
+ resPageMsg.getString("cannot_be_blank_if_VALIDATION_not_blank"));
htmlErrors.put(j + "," + k + ",18", resPageMsg.getString("required_field"));
}
if (regexpError != null && regexpError.length() > 255) {
errors.add(resPageMsg.getString("regexp_errror_length_error"));
}
boolean phiBoolean = false;
cell = sheet.getRow(k).getCell((short) 19);
// String phi = getValue(cell);
String phi = "";
if (cell.getCellType() == HSSFCell.CELL_TYPE_NUMERIC) {
double dphi = cell.getNumericCellValue();
if ((dphi - (int) dphi) * 1000 == 0) {
phi = (int) dphi + "";
}
}
if (!"0".equals(phi) && !"1".equals(phi)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("PHI_column") + resPageMsg.getString("was_invalid_at_row") + k
+ ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("PHI_column") + " "
+ resPageMsg.getString("can_only_be_either_0_or_1"));
htmlErrors.put(j + "," + k + ",19", resPageMsg.getString("INVALID_VALUE"));
} else {
phiBoolean = "1".equals(phi) ? true : false;
}
boolean isRequired = false;
cell = sheet.getRow(k).getCell((short) 20);
String required = getValue(cell);
logger.info(getValue(cell));
// does the above no longer work???
// String required = "";
if (StringUtil.isBlank(required)) {
required = "0";
} else if (cell.getCellType() == HSSFCell.CELL_TYPE_NUMERIC) {
double dr = cell.getNumericCellValue();
if ((dr - (int) dr) * 1000 == 0) {
required = (int) dr + "";
}
}
if (!"0".equals(required) && !"1".equals(required)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("REQUIRED_column") + " "
+ resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". "
+ resPageMsg.getString("REQUIRED_column") + resPageMsg.getString("can_only_be_either_0_or_1"));
htmlErrors.put(j + "," + k + ",20", resPageMsg.getString("INVALID_VALUE"));
} else {
isRequired = "1".equals(required) ? true : false;
}
// Create oid for Item Bean
String itemOid = idao.getValidOid(new ItemBean(), crfName, itemName, itemOids);
itemOids.add(itemOid);
// better spot for checking item might be right here,
// tbh 7-25
String vlSql = "";
if (dbName.equals("oracle")) {
vlSql =
"INSERT INTO ITEM (NAME,DESCRIPTION,UNITS,PHI_STATUS,"
+ "ITEM_DATA_TYPE_ID, ITEM_REFERENCE_TYPE_ID,STATUS_ID,OWNER_ID,DATE_CREATED,OC_OID) " + "VALUES ('"
+ stripQuotes(itemName) + "','" + stripQuotes(descLabel) + "','" + stripQuotes(unit) + "'," + (phiBoolean == true ? 1 : 0)
+ "," + dataTypeIdString + ",1,1," + ub.getId() + ", sysdate" + ",'" + itemOid + "')";
} else {
vlSql =
"INSERT INTO ITEM (NAME,DESCRIPTION,UNITS,PHI_STATUS,"
+ "ITEM_DATA_TYPE_ID, ITEM_REFERENCE_TYPE_ID,STATUS_ID,OWNER_ID,DATE_CREATED,OC_OID) " + "VALUES ('"
+ stripQuotes(itemName) + "','" + stripQuotes(descLabel) + "','" + stripQuotes(unit) + "'," + phiBoolean + ","
+ dataTypeIdString + ",1,1," + ub.getId() + ", NOW()" + ",'" + itemOid + "')";
}
backupItemQueries.put(itemName, vlSql);
// to compare items from DB later, if two items have the
// same name,
// but different units or phiStatus, they are different
ItemBean ib = new ItemBean();
ib.setName(itemName);
ib.setUnits(unit);
ib.setPhiStatus(phiBoolean);
ib.setDescription(descLabel);
ib.setDataType(ItemDataType.getByName(dataType.toLowerCase()));
// put metadata into item
ResponseSetBean rsb = new ResponseSetBean();
// notice that still "\\," in options - jxu-08-31-06
String resOptions1 = resOptions.replaceAll("\\\\,", "\\,");
String resValues1 = resValues.replaceAll("\\\\,", "\\,");
rsb.setOptions(stripQuotes(resOptions1), stripQuotes(resValues1));
ItemFormMetadataBean ifmb = new ItemFormMetadataBean();
ifmb.setResponseSet(rsb);
ib.setItemMeta(ifmb);
items.put(itemName, ib);
int ownerId = ub.getId();
if (!itemCheck.containsKey(itemName)) {// item not in
// the DB
openQueries.put(itemName, vlSql);
} else {// item in the DB
ItemBean oldItem = (ItemBean) idao.findByNameAndCRFId(itemName, crfId);
if (oldItem.getOwnerId() == ub.getId()) {// owner
// can
// update
if (!cvdao.hasItemData(oldItem.getId())) {// no
// item
// data
String upSql = "";
if (dbName.equals("oracle")) {
upSql =
"UPDATE ITEM SET DESCRIPTION='" + stripQuotes(descLabel) + "'," + "UNITS='" + stripQuotes(unit) + "',"
+ "PHI_STATUS=" + (phiBoolean ? 1 : 0) + "," + "ITEM_DATA_TYPE_ID=" + dataTypeIdString
+ " WHERE exists (SELECT versioning_map.item_id from versioning_map, crf_version where"
+ " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id= " + crfId
+ " AND item.item_id = versioning_map.item_id)" + " AND item.name='" + stripQuotes(itemName)
+ "' AND item.owner_id = " + ownerId;
} else {
upSql =
"UPDATE ITEM SET DESCRIPTION='" + stripQuotes(descLabel) + "'," + "UNITS='" + stripQuotes(unit) + "',"
+ "PHI_STATUS=" + phiBoolean + "," + "ITEM_DATA_TYPE_ID=" + dataTypeIdString
+ " FROM versioning_map, crf_version" + " WHERE item.name='" + stripQuotes(itemName) + "' AND item.owner_id = "
+ ownerId + " AND item.item_id = versioning_map.item_id AND"
+ " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id = " + crfId;
}// end of if dbname
openQueries.put(itemName, upSql);
} else {
String upSql = "";
if (dbName.equals("oracle")) {
upSql =
"UPDATE ITEM SET DESCRIPTION='" + stripQuotes(descLabel) + "'," + "PHI_STATUS=" + (phiBoolean ? 1 : 0)
+ " WHERE exists (SELECT versioning_map.item_id from versioning_map, crf_version where"
+ " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id= " + crfId
+ " AND item.item_id = versioning_map.item_id)" + " AND item.name='" + stripQuotes(itemName)
+ "' AND item.owner_id = " + ownerId;
} else {
upSql =
"UPDATE ITEM SET DESCRIPTION='" + stripQuotes(descLabel) + "'," + "PHI_STATUS=" + phiBoolean
+ " FROM versioning_map, crf_version" + " WHERE item.name='" + stripQuotes(itemName) + "' AND item.owner_id = "
+ ownerId + " AND item.item_id = versioning_map.item_id AND"
+ " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id = " + crfId;
}// end of if dbName
openQueries.put(itemName, upSql);
}
} else {
ownerId = oldItem.getOwner().getId();
}
}
String sql = "";
if (dbName.equals("oracle")) {
// resOptions = resOptions.replaceAll("\\\\,",
// "\\,");
sql =
"INSERT INTO RESPONSE_SET (LABEL, OPTIONS_TEXT, OPTIONS_VALUES, " + "RESPONSE_TYPE_ID, VERSION_ID)" + " VALUES ('"
+ stripQuotes(responseLabel) + "', '" + stripQuotes(resOptions.replaceAll("\\\\,", "\\,")) + "','"
+ stripQuotes(resValues.replace("\\\\", "\\")) + "'," + "(SELECT RESPONSE_TYPE_ID From RESPONSE_TYPE Where NAME='"
+ stripQuotes(responseType.toLowerCase()) + "')," + versionIdString + ")";
} else {
sql =
"INSERT INTO RESPONSE_SET (LABEL, OPTIONS_TEXT, OPTIONS_VALUES, " + "RESPONSE_TYPE_ID, VERSION_ID)" + " VALUES ('"
+ stripQuotes(responseLabel) + "', E'" + stripQuotes(resOptions) + "', E'" + stripQuotes(resValues) + "',"
+ "(SELECT RESPONSE_TYPE_ID From RESPONSE_TYPE Where NAME='" + stripQuotes(responseType.toLowerCase()) + "'),"
+ versionIdString + ")";
}
if (!resNames.contains(responseLabel)) {
queries.add(sql);
resNames.add(responseLabel);
// this will have to change since we have some data
// in the actual
// spreadsheet
// change it to caching response set names in a
// collection?
// or just delete the offending cells from the
// spreadsheet?
}
String parentItemString = "0";
if (!StringUtil.isBlank(parentItem)) {
if (dbName.equals("oracle")) {
parentItemString =
"(SELECT MAX(ITEM_ID) FROM ITEM WHERE NAME='" + stripQuotes(parentItem) + "' AND owner_id = " + ownerId + " )";
} else {
parentItemString =
"(SELECT ITEM_ID FROM ITEM WHERE NAME='" + stripQuotes(parentItem) + "' AND owner_id = " + ownerId
+ " ORDER BY OC_OID DESC LIMIT 1)";
}
}
String selectCorrectItemQueryPostgres =
" (SELECT I.ITEM_ID FROM ITEM I LEFT OUTER JOIN ITEM_FORM_METADATA IFM ON I.ITEM_Id = IFM.ITEM_ID LEFT OUTER JOIN CRF_VERSION CV ON IFM.CRF_VERSION_ID = CV.CRF_VERSION_ID WHERE "
+ " ( I.NAME='"
+ itemName
+ "'"
+ " AND I.owner_id = "
+ ownerId
+ " AND CV.CRF_VERSION_ID is null )"
+ " OR "
+ " ( I.NAME='"
+ itemName
+ "'"
+ " AND I.owner_id = "
+ ownerId
+ " AND CV.CRF_VERSION_ID is not null AND CV.CRF_ID ="
+ crfId
+ " ) "
+ " ORDER BY I.OC_ID DESC LIMIT 1) ";
String selectCorrectItemQueryOracle =
" (SELECT MAX(I.ITEM_ID) FROM ITEM I LEFT OUTER JOIN ITEM_FORM_METADATA IFM ON I.ITEM_Id = IFM.ITEM_ID LEFT OUTER JOIN CRF_VERSION CV ON IFM.CRF_VERSION_ID = CV.CRF_VERSION_ID WHERE "
+ " ( I.NAME='"
+ itemName
+ "'"
+ " AND I.owner_id = "
+ ownerId
+ " AND CV.CRF_VERSION_ID is null )"
+ " OR "
+ " ( I.NAME='"
+ itemName + "'" + " AND I.owner_id = " + ownerId + " AND CV.CRF_VERSION_ID is not null AND CV.CRF_ID =" + crfId + " )) ";
String sql2 = "";
if (dbName.equals("oracle")) {
sql2 =
"INSERT INTO ITEM_FORM_METADATA (CRF_VERSION_ID, RESPONSE_SET_ID," + "ITEM_ID,SUBHEADER,header,LEFT_ITEM_TEXT,"
+ "RIGHT_ITEM_TEXT,PARENT_ID,SECTION_ID,ORDINAL,PARENT_LABEL,COLUMN_NUMBER,PAGE_NUMBER_LABEL,question_number_label,"
+ "REGEXP,REGEXP_ERROR_MSG,REQUIRED)" + " VALUES ("
+ versionIdString
+ ",(SELECT RESPONSE_SET_ID FROM RESPONSE_SET WHERE LABEL='"
+ stripQuotes(responseLabel)
+ "'"
+ " AND VERSION_ID="
+ versionIdString
+ "),"
+ selectCorrectItemQueryOracle
+ ",'"
+ stripQuotes(subHeader)
+ "','"
+ stripQuotes(header)
+ "','"
+ stripQuotes(leftItemText)
+ "','"
+ stripQuotes(rightItemText)
+ "',"
+ parentItemString
+ ", (SELECT SECTION_ID FROM SECTION WHERE LABEL='"
+ secName
+ "' AND "
+ "CRF_VERSION_ID IN "
+ versionIdString
+ "), "
+ k
+ ",'"
+ parentItem
+ "',"
+ columnNum
+ ",'"
+ stripQuotes(page)
+ "','"
+ stripQuotes(questionNum)
+ "','"
+ stripQuotes(regexp1) + "','" + stripQuotes(regexpError) + "', " + (isRequired ? 1 : 0) + ")";
logger.warn(sql2);
} else {
sql2 =
"INSERT INTO ITEM_FORM_METADATA (CRF_VERSION_ID, RESPONSE_SET_ID," + "ITEM_ID,SUBHEADER,HEADER,LEFT_ITEM_TEXT,"
+ "RIGHT_ITEM_TEXT,PARENT_ID,SECTION_ID,ORDINAL,PARENT_LABEL,COLUMN_NUMBER,PAGE_NUMBER_LABEL,question_number_label,"
+ "REGEXP,REGEXP_ERROR_MSG,REQUIRED)" + " VALUES ("
+ versionIdString
+ ",(SELECT RESPONSE_SET_ID FROM RESPONSE_SET WHERE LABEL='"
+ stripQuotes(responseLabel)
+ "'"
+ " AND VERSION_ID="
+ versionIdString
+ "),"
+ selectCorrectItemQueryPostgres
+ ",'"
+ stripQuotes(subHeader)
+ "','"
+ stripQuotes(header)
+ "','"
+ stripQuotes(leftItemText)
+ "','"
+ stripQuotes(rightItemText)
+ "',"
+ parentItemString
+ ", (SELECT SECTION_ID FROM SECTION WHERE LABEL='"
+ secName
+ "' AND "
+ "CRF_VERSION_ID IN "
+ versionIdString
+ "), "
+ k
+ ",'"
+ parentItem
+ "',"
+ columnNum
+ ",'"
+ stripQuotes(page)
+ "','"
+ stripQuotes(questionNum)
+ "','"
+ stripQuotes(regexp1) + "','" + stripQuotes(regexpError) + "', " + isRequired + ")";
}
queries.add(sql2);
// link version with items now
String sql3 = "";
if (dbName.equals("oracle")) {
sql3 =
"INSERT INTO VERSIONING_MAP (CRF_VERSION_ID, ITEM_ID) VALUES ( " + versionIdString + "," + selectCorrectItemQueryOracle + ")";
} else {
sql3 =
"INSERT INTO VERSIONING_MAP (CRF_VERSION_ID, ITEM_ID) VALUES ( " + versionIdString + "," + selectCorrectItemQueryPostgres + ")";
}
queries.add(sql3);
// this item doesn't have group, so put it into
// 'Ungrouped' group
String sqlGroupLabel = "";
if (dbName.equals("oracle")) {
sqlGroupLabel =
"INSERT INTO ITEM_GROUP_METADATA (" + "item_group_id,header," + "subheader, layout, repeat_number, repeat_max,"
+ " repeat_array,row_start_number, crf_version_id," + "item_id , ordinal, borders) VALUES ("
+ "(SELECT MAX(ITEM_GROUP_ID) FROM ITEM_GROUP WHERE NAME='Ungrouped' AND crf_id = "
+ crfId
+ " ),'"
+ ""
+ "', '"
+ ""
+ "', '"
+ ""
+ "', "
+ 1
+ ", "
+ 1
+ ", '', 1,"
+ versionIdString
+ ","
// + "(SELECT MAX(ITEM_ID) FROM ITEM WHERE
// NAME='"
// + itemName + "' ),"
+ "(SELECT MAX(ITEM.ITEM_ID) FROM ITEM,ITEM_FORM_METADATA,CRF_VERSION WHERE ITEM.NAME='"
+ itemName
+ "' "
+ "AND ITEM.ITEM_ID = ITEM_FORM_METADATA.ITEM_ID and ITEM_FORM_METADATA.CRF_VERSION_ID=CRF_VERSION.CRF_VERSION_ID "
+ "AND CRF_VERSION.CRF_ID= " + crfId + " )," + k + ",0)";
} else {
sqlGroupLabel =
"INSERT INTO ITEM_GROUP_METADATA (" + "item_group_id,HEADER," + "subheader, layout, repeat_number, repeat_max,"
+ " repeat_array,row_start_number, crf_version_id," + "item_id , ordinal, borders) VALUES ("
+ "(SELECT ITEM_GROUP_ID FROM ITEM_GROUP WHERE NAME='Ungrouped' AND crf_id = "
+ crfId
+ " ORDER BY oc_oid DESC LIMIT 1),'"
+ ""
+ "', '"
+ ""
+ "', '"
+ ""
+ "', "
+ 1
+ ", "
+ 1
+ ", '', 1,"
+ versionIdString
+ ","
// + "(SELECT ITEM_ID FROM ITEM WHERE
// NAME='" + itemName + "' ORDER BY OID DESC
// LIMIT 1),"
+ "(SELECT ITEM.ITEM_ID FROM ITEM,ITEM_FORM_METADATA,CRF_VERSION WHERE ITEM.NAME='"
+ itemName
+ "' "
+ "AND ITEM.ITEM_ID = ITEM_FORM_METADATA.ITEM_ID and ITEM_FORM_METADATA.CRF_VERSION_ID=CRF_VERSION.CRF_VERSION_ID "
+ "AND CRF_VERSION.CRF_ID= " + crfId + " ORDER BY ITEM.OC_OID DESC LIMIT 1)," + k + ",0)";
}
queries.add(sqlGroupLabel);
}
} else if (sheetName.equalsIgnoreCase("Sections")) {
logger.info("read sections");
// multiple rows, six cells, last one is number
for (int k = 1; k < numRows; k++) {
if (blankRowCount == 5) {
logger.info("hit end of the row ");
break;
}
if (sheet.getRow(k) == null) {
blankRowCount++;
continue;
}
HSSFCell cell = sheet.getRow(k).getCell((short) 0);
String secLabel = getValue(cell);
secLabel = secLabel.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(secLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column") + " "
+ resPageMsg.getString("was_blank_at_row") + k + " " + ", " + resPageMsg.getString("sections_worksheet") + ".");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("required_field"));
}
if (secLabel != null && secLabel.length() > 2000) {
errors.add(resPageMsg.getString("section_label_length_error"));
}
if (secNames.contains(secLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column")
+ resPageMsg.getString("was_a_duplicate_of") + secLabel + " " + resPageMsg.getString("at_row") + " " + k + ", "
+ resPageMsg.getString("sections_worksheet") + ".");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("DUPLICATE_FIELD"));
}
// logger.info("section name:" + secLabel + "row num:"
// +k);
secNames.add(secLabel);
cell = sheet.getRow(k).getCell((short) 1);
String title = getValue(cell);
title = title.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(title)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_TITLE_column") + " "
+ resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("sections_worksheet") + ".");
htmlErrors.put(j + "," + k + ",1", resPageMsg.getString("required_field"));
}
if (title != null && title.length() > 2000) {
errors.add(resPageMsg.getString("section_title_length_error"));
}
cell = sheet.getRow(k).getCell((short) 2);
String subtitle = getValue(cell);
if (subtitle != null && subtitle.length() > 2000) {
errors.add(resPageMsg.getString("section_subtitle_length_error"));
}
cell = sheet.getRow(k).getCell((short) 3);
String instructions = getValue(cell);
if (instructions != null && instructions.length() > 2000) {
errors.add(resPageMsg.getString("section_instruction_length_error"));
}
cell = sheet.getRow(k).getCell((short) 4);
String pageNumber = getValue(cell);
if (pageNumber != null && pageNumber.length() > 5) {
errors.add(resPageMsg.getString("section_page_number_length_error"));
}
cell = sheet.getRow(k).getCell((short) 5);
String parentSection = getValue(cell);
parentSection = parentSection.replaceAll("<[^>]*>", "");
if (!StringUtil.isBlank(parentSection)) {
try {
parentId = Integer.parseInt(parentSection);
} catch (NumberFormatException ne) {
parentId = 0;
}
}
String sql = "";
if (dbName.equals("oracle")) {
sql =
"INSERT INTO SECTION (CRF_VERSION_ID," + "STATUS_ID,LABEL, TITLE, INSTRUCTIONS, SUBTITLE, PAGE_NUMBER_LABEL,"
+ "ORDINAL, PARENT_ID, OWNER_ID, DATE_CREATED) " + "VALUES (" + versionIdString + ",1,'" + secLabel + "','"
+ stripQuotes(title) + "', '" + stripQuotes(instructions) + "', '" + stripQuotes(subtitle) + "','" + pageNumber + "'," + k
+ "," + parentId + "," + ub.getId() + ",sysdate)";
} else {
sql =
"INSERT INTO SECTION (CRF_VERSION_ID," + "STATUS_ID,LABEL, TITLE, INSTRUCTIONS, SUBTITLE, PAGE_NUMBER_LABEL,"
+ "ORDINAL, PARENT_ID, OWNER_ID, DATE_CREATED) " + "VALUES (" + versionIdString + ",1,'" + secLabel + "','"
+ stripQuotes(title) + "', '" + stripQuotes(instructions) + "', '" + stripQuotes(subtitle) + "','" + pageNumber + "'," + k
+ "," + parentId + "," + ub.getId() + ",NOW())";
}
queries.add(sql);
}// end for loop
} else if (sheetName.equalsIgnoreCase("CRF")) {
logger.info("read crf");
// one row, four cells, all strings
if (sheet == null || sheet.getRow(1) == null || sheet.getRow(1).getCell((short) 0) == null) {
throw new CRFReadingException("Blank row found in sheet CRF.");
}
HSSFCell cell = sheet.getRow(1).getCell((short) 0);
crfName = getValue(cell);
crfName = crfName.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(crfName)) {
// errors.add(resPageMsg.getString("the") + " " +
// resPageMsg.getString("CRF_NAME_column")
// +
// resPageMsg.getString("was_blank_in_the_CRF_worksheet"));
// htmlErrors.put(j + ",1,0",
// resPageMsg.getString("required_field"));
throw new CRFReadingException("The CRF_NAME column was blank in the CRF worksheet.");
}
if (crfName.length() > 255) {
errors.add(resPageMsg.getString("crf_name_length_error"));
}
CRFBean existingCRFWithSameName = (CRFBean) cdao.findByName(crfName);
if (this.getCrfId() == 0) {
if (existingCRFWithSameName.getName() != null && existingCRFWithSameName.getName().equals(crfName)) {
errors.add(resPageMsg.getString("crf_name_already_used"));
}
}
// TODO Why the following codes are commented out? -jxu
// try {
// CRFBean checkName = (CRFBean) cdao.findByPK(crfId);
// if (!checkName.getName().equals(crfName)) {
// logger.info("crf name is mismatch");
// errors.add(resPageMsg.getString("the") + " " +
// resPageMsg.getString("CRF_NAME_column") +
// resPageMsg.getString("did_not_match_crf_version") + " '"
// + checkName.getName()
// + "' " + resPageMsg.getString("before_you_continue"));
// htmlErrors.put(j + ",1,0",
// resPageMsg.getString("DID_NOT_MATCH_CRF"));
// }
// } catch (Exception pe) {
// logger.warn("Exception happened when check CRF name" +
// pe.getMessage());
// }
cell = sheet.getRow(1).getCell((short) 1);
String version = getValue(cell);
version = version.replaceAll("<[^>]*>", "");
ncrf.setVersionName(version);
if (version != null && version.length() > 255) {
errors.add(resPageMsg.getString("version_length_error"));
}
// YW, 08-22-2007, since versionName is now obtained from
// spreadsheet,
// blank check has been moved to
// CreateCRFVersionServlet.java
// and mismatch check is not necessary
// if (StringUtil.isBlank(version)) {
// errors.add("The VERSION column was blank in the CRF
// worksheet.");
// htmlErrors.put(j + ",1,1", "REQUIRED FIELD");
// }else if (!version.equals(versionName)) {
// errors.add("The VERSION column did not match the intended
// version name "
// + "you want to upload. Make sure this reads '" +
// versionName
// + "' before you continue.");
// htmlErrors.put(j + ",1,1", "DID NOT MATCH VERSION");
// }
cell = sheet.getRow(1).getCell((short) 2);
String versionDesc = getValue(cell);
versionDesc = versionDesc.replaceAll("<[^>]*>", "");
if (versionDesc != null && versionDesc.length() > 4000) {
errors.add(resPageMsg.getString("version_description_length_error"));
}
cell = sheet.getRow(1).getCell((short) 3);
String revisionNotes = getValue(cell);
revisionNotes = revisionNotes.replaceAll("<[^>]*>", "");
if (revisionNotes != null && revisionNotes.length() > 255) {
errors.add(resPageMsg.getString("revision_notes_length_error"));
}
if (StringUtil.isBlank(revisionNotes)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("REVISION_NOTES_column") + " "
+ resPageMsg.getString("was_blank_in_the_CRF_worksheet"));
htmlErrors.put(j + ",1,3", resPageMsg.getString("required_field"));
}
// Generating query string for the new CRF
Connection con = null;
String crfOid = null;
if (crfId == 0) {
crfOid = cdao.getValidOid(new CRFBean(), crfName);
int nextCRFId;
try {
con = ds.getConnection();
CoreResources.setSchema(con);
/*
* We are selecting the crf id which will be used to
* save the new CRF. Selecting the crf id in advance
* will not cause any problem in a multi threaded
* environment because the nextVal() method always
* returns unique values. So there is no chance of
* processing two CRF simultaneously with same crf
* id.
*/
ResultSet nextIdRs;
if (dbName.equals("oracle")) {
nextIdRs = con.createStatement().executeQuery("select crf_id_seq.nextval from dual");
} else {
nextIdRs = con.createStatement().executeQuery("select nextval('crf_crf_id_seq')");
}
nextIdRs.next();
nextCRFId = nextIdRs.getInt(1);
crfId = nextCRFId;
ncrf.setCrfId(crfId);
String createCRFSql = "";
if (dbName.equals("oracle")) {
createCRFSql =
"INSERT INTO CRF (CRF_ID, STATUS_ID, NAME, DESCRIPTION, OWNER_ID, DATE_CREATED, OC_OID, SOURCE_STUDY_ID) VALUES (" + crfId
+ ", 1,'" + stripQuotes(crfName) + "','" + stripQuotes(versionDesc) + "'," + ub.getId() + ",sysdate" + ",'" + crfOid
+ "'," + studyId + ")";
} else {
createCRFSql =
"INSERT INTO CRF (CRF_ID, STATUS_ID, NAME, DESCRIPTION, OWNER_ID, DATE_CREATED, OC_OID, SOURCE_STUDY_ID) VALUES (" + crfId
+ ", 1,'" + stripQuotes(crfName) + "','" + stripQuotes(versionDesc) + "'," + ub.getId() + ",NOW()" + ",'" + crfOid
+ "'," + studyId + ")";
}
queries.add(createCRFSql);
} catch (SQLException e) {
logger.warn("Exception encountered with query select nextval('crf_crf_id_seq'), Message-" + e.getMessage());
} finally {
if (con != null) {
try {
con.close();
} catch (SQLException e) {
logger.warn("Connectin can't be closed");
}
}
}
}
// check for instrument existence here??? tbh 7/28
// engaging in new validation, tbh, 6-4-04
// modify nib.getinstversions to look for version name and
// description
// need to stop uploads of same name-description pairs
HashMap checkCRFVersions = ncrf.getCrfVersions();
// this now returns a hash map of key:version_name
// ->value:version_description
boolean overwrite = false;
if (checkCRFVersions.containsKey(version)) {
logger.info("found a matching version name..." + version);
errors.add(resPageMsg.getString("version_not_unique_cause_confusion"));
htmlErrors.put(j + ",1,2", resPageMsg.getString("NOT_UNIQUE"));
}
// Create oid for Crf Version
String oid;
if (crfOid != null) {
oid = cvdao.getValidOid(new CRFVersionBean(), crfOid, version);
} else {
CRFBean crfBean = (CRFBean) cdao.findByName(crfName);
oid = cvdao.getValidOid(new CRFVersionBean(), crfBean.getOid(), version);
}
String sql = "";
if (dbName.equals("oracle")) {
logger.warn("TEST 2");
if (crfId == 0) {
sql =
"INSERT INTO CRF_VERSION (NAME, DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) "
+ "VALUES ('" + stripQuotes(version) + "','" + stripQuotes(versionDesc) + "'," + "(SELECT CRF_ID FROM CRF WHERE NAME='"
+ crfName + "'),1,sysdate," + ub.getId() + ",'" + stripQuotes(revisionNotes) + "','" + oid + "')";
} else {
sql =
"INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + "VALUES ('"
+ version + "','" + stripQuotes(versionDesc) + "'," + crfId + ",1,sysdate," + ub.getId() + ",'"
+ stripQuotes(revisionNotes) + "','" + oid + "')";
}
} else {
if (crfId == 0) {
sql =
"INSERT INTO CRF_VERSION (NAME, DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) "
+ "VALUES ('" + stripQuotes(version) + "','" + stripQuotes(versionDesc) + "'," + "(SELECT CRF_ID FROM CRF WHERE NAME='"
+ crfName + "'),1,NOW()," + ub.getId() + ",'" + stripQuotes(revisionNotes) + "','" + oid + "')";
} else {
sql =
"INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + "VALUES ('"
+ version + "','" + stripQuotes(versionDesc) + "'," + crfId + ",1,NOW()," + ub.getId() + ",'" + stripQuotes(revisionNotes)
+ "','" + oid + "')";
}
}
queries.add(sql);
for (int i = 0; i < queries.size(); i++) {
String s = (String) queries.get(i);
logger.info("====================" + s);
}
pVersion = version;
pVerDesc = versionDesc;
}
versionIdString = "(SELECT CRF_VERSION_ID FROM CRF_VERSION WHERE NAME ='" + pVersion + "' AND CRF_ID=" + crfId + ")";
// move html creation to here, include error creation as well,
// tbh 7/28
buf.append(sheetName + "<br>");
buf
.append("<div class=\"box_T\"><div class=\"box_L\"><div class=\"box_R\"><div class=\"box_B\"><div class=\"box_TL\"><div class=\"box_TR\"><div class=\"box_BL\"><div class=\"box_BR\">");
buf.append("<div class=\"textbox_center\">");
buf.append("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\" width=\"100%\"");
buf.append("caption=\"" + wb.getSheetName(j) + "\"" + ">");
for (int i = 0; i < numRows; i++) {
buf.append("<tr>");
if (sheet.getRow(i) == null) {
continue;
}
int numCells = sheet.getRow(i).getLastCellNum();
for (int y = 0; y < numCells; y++) {
HSSFCell cell = sheet.getRow(i).getCell((short) y);
int cellType = 0;
String error = " ";
String errorKey = j + "," + i + "," + y;
if (htmlErrors.containsKey(errorKey)) {
error = "<span class=\"alert\">" + htmlErrors.get(errorKey) + "</span>";
}
if (cell == null) {
cellType = HSSFCell.CELL_TYPE_BLANK;
} else {
cellType = cell.getCellType();
}
switch (cellType) {
case HSSFCell.CELL_TYPE_BLANK:
buf.append("<td class=\"table_cell\">" + error + "</td>");
break;
case HSSFCell.CELL_TYPE_NUMERIC:
buf.append("<td class=\"table_cell\">" + cell.getNumericCellValue() + " " + error + "</td>");
break;
case HSSFCell.CELL_TYPE_STRING:
buf.append("<td class=\"table_cell\">" + cell.getStringCellValue() + " " + error + "</td>");
break;
default:
buf.append("<td class=\"table_cell\">" + error + "</td>");
}
}
buf.append("</tr>");
}
buf.append("</table>");
buf.append("<br></div>");
buf.append("</div></div></div></div></div></div></div></div>");
buf.append("</div><br>");
}// end of the else sheet loop
}// end of the for loop for sheets
ncrf.setQueries(queries);
ncrf.setItemQueries(openQueries);
ncrf.setBackupItemQueries(backupItemQueries);
ncrf.setItems(items);
if (!errors.isEmpty()) {
ncrf.setErrors(errors);
}
// logger.info("html table:" + buf.toString());
ncrf.setHtmlTable(buf.toString());
return ncrf;
}
/**
* stripQuotes, utility function meant to replace single quotes in strings
* with double quotes for SQL compatability. Don't -> Don''t, for example.
*
* @param subj
* the subject line
* @return A string with all the quotes escaped.
*/
public String stripQuotes(String subj) {
if (subj == null) {
return null;
}
String returnme = "";
String[] subjarray = subj.split("'");
if (subjarray.length == 1) {
returnme = subjarray[0];
} else {
for (int i = 0; i < subjarray.length - 1; i++) {
returnme += subjarray[i];
returnme += "''";
}
returnme += subjarray[subjarray.length - 1];
}
return returnme;
}
public String getValue(HSSFCell cell) {
String val = null;
int cellType = 0;
if (cell == null) {
cellType = HSSFCell.CELL_TYPE_BLANK;
} else {
cellType = cell.getCellType();
}
switch (cellType) {
case HSSFCell.CELL_TYPE_BLANK:
val = "";
break;
case HSSFCell.CELL_TYPE_NUMERIC:
// YW << Modify code so that floating number alone can be used for
// CRF version. Before it must use, e.g. v1.1
// Meanwhile modification has been done for read PHI cell and
// Required cell
val = cell.getNumericCellValue() + "";
logger.info("found a numeric cell: " + val);
// what if the version is a whole number? added other code below
// from PHI, tbh 6/5/07
// So now we also treat 3, 3.0, 3.00 as same as 3. If users want 3.0
// or 3.10 the best way is use String type. -YW
// >> YW
double dphi = cell.getNumericCellValue();
if ((dphi - (int) dphi) * 1000 == 0) {
val = (int) dphi + "";
}
logger.info("found a numeric cell after transfer: " + val);
// buf.append("<td><font class=\"bodytext\">" +
// cell.getNumericCellValue()
// + "</font></td>");
break;
case HSSFCell.CELL_TYPE_STRING:
val = cell.getStringCellValue();
if (val.matches("'")) {
// logger.info("Found single quote! "+val);
val.replaceAll("'", "''");
}
// buf.append("<td><font class=\"bodytext\">" +
// cell.getStringCellValue()
// + "</font></td>");
break;
default:
val = "";
// buf.append("<td></td>");
}
// logger.info("final val returned: "+val);
return val.trim();
}
public String toHTML(int sheetIndex) throws IOException {
StringBuffer buf = new StringBuffer();
HSSFWorkbook wb = new HSSFWorkbook(fs);
int numSheets = wb.getNumberOfSheets();
for (int j = 0; j < numSheets; j++) {
HSSFSheet sheet = wb.getSheetAt(j);// sheetIndex);
String sheetName = wb.getSheetName(j);
buf.append(sheetName + "<br>");
buf.append("<table border=\"2\"");
buf.append("caption=\"" + wb.getSheetName(sheetIndex) + "\"" + ">");
int numCols = sheet.getPhysicalNumberOfRows();
for (int i = 0; i < numCols; i++) {
buf.append("<tr>");
if (sheet.getRow(i) == null) {
continue;
}
int numCells = sheet.getRow(i).getLastCellNum();
for (int y = 0; y < numCells; y++) {
HSSFCell cell = sheet.getRow(i).getCell((short) y);
int cellType = 0;
if (cell == null) {
cellType = HSSFCell.CELL_TYPE_BLANK;
} else {
cellType = cell.getCellType();
}
switch (cellType) {
case HSSFCell.CELL_TYPE_BLANK:
buf.append("<td> </td>");
break;
case HSSFCell.CELL_TYPE_NUMERIC:
buf.append("<td>" + cell.getNumericCellValue() + "</td>");
break;
case HSSFCell.CELL_TYPE_STRING:
buf.append("<td>" + cell.getStringCellValue() + "</td>");
break;
default:
buf.append("<td></td>");
}
}
buf.append("</tr>");
}
buf.append("</table>");
}// end of sheet count, added by tbh 5-31
return buf.toString();
}
private String getMUInsertSql(String oid, String measurementUnitName, int ownerId, String dbName) {
return "insert into measurement_unit (oc_oid, name) values ('" + oid + "', '" + stripQuotes(measurementUnitName) + "')";
}
public void setLocale(Locale locale) {
this.locale = locale;
}
public Locale getLocale() {
return this.locale;
}
public MeasurementUnitDao getMeasurementUnitDao() {
return measurementUnitDao;
}
public void setMeasurementUnitDao(MeasurementUnitDao measurementUnitDao) {
this.measurementUnitDao = measurementUnitDao;
}
}