Java tutorial
/* * 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.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(); /* * 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; } }