Examples with ScoreException org.akaza.openclinica.exception.ScoreException used on opensource projects

Example 1 with ScoreException

use of org.akaza.openclinica.exception.ScoreException in project OpenClinica by OpenClinica.

the class ScoreCalculator method redoCalculations.

/**
     * Re-do calculations if funcs include changed item(s) and funcs are not
     * included in the current section. If calculation can not sucessfully redo,
     * old value will be erased and "<erased>" will be saved in database. <br>
     * The parameter 'itemdata' might be overwritten.
     * 
     * @param itemGroupSizes
     * @param items
     * @param itemdata
     * @param oldItemdata
     * @param updatedData
     * @param sectionId
     * @return ArrayList<String> which records left_item_text of items who
     *         failed to be updated into database.
     */
public ArrayList<String> redoCalculations(HashMap<String, ItemBean> items, HashMap<String, String> itemdata, TreeSet<String> changedItems, HashMap<Integer, TreeSet<Integer>> itemOrdinals, int sectionId) {
    ArrayList<String> updateFailedItems = new ArrayList<String>();
    if (itemdata == null) {
        logger.error("In ScoreCalculator redoCalculations(), itemdata is empty!");
        errors.add("In ScoreCalculator redoCalculations(), 'itemdata' map is empty!");
        return updateFailedItems;
    }
    if (changedItems == null) {
        logger.error("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
        errors.add("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
        return updateFailedItems;
    }
    ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
    NumberFormat nf = NumberFormat.getInstance();
    Parser parser = new Parser(items, itemdata);
    try {
        // for calculation type
        List<ItemFormMetadataBean> derivedItemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
        if (derivedItemList.size() > 0) {
            Collections.sort(derivedItemList);
            for (ItemFormMetadataBean ifmb : derivedItemList) {
                if (ifmb.getSectionId() != sectionId) {
                    ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
                    ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
                    int groupsize = 1;
                    if (itemOrdinals.containsKey(ib.getId())) {
                        groupsize = itemOrdinals.get(ib.getId()).size();
                    }
                    String value = "";
                    ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
                    for (int i = 0; i < groupsize; ++i) {
                        ItemDataBean idb = iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), i + 1);
                        // is there any changed item
                        Parser p = new Parser(items, itemdata);
                        parsedExp = parser.parseScoreTokens(rob.getValue());
                        if (p.isChanged(changedItems, parsedExp)) {
                            StringBuffer err = new StringBuffer();
                            parsedExp = parser.assignVariables(parsedExp, i + 1);
                            // before, set "<erased>"
                            if (parser.getErrors().length() > 0) {
                                err.append(parser.getErrors());
                                if (idb.isActive()) {
                                    idb.setValue("<erased>");
                                    idb.setStatus(Status.UNAVAILABLE);
                                    idb = (ItemDataBean) iddao.update(idb);
                                    if (!idb.isActive()) {
                                        String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                                        updateFailedItems.add(key);
                                    }
                                }
                                parser.setErrors(new StringBuffer());
                            } else // otherwise do calculation
                            {
                                try {
                                    value = ScoreUtil.eval(parsedExp);
                                } catch (ScoreException se) {
                                    logger.error(se.getMessage());
                                }
                                String exp = rob.getValue();
                                exp = exp.replace("##", ",");
                                if (writeToDB(ib, ifmb, idb, exp, value, err)) {
                                    changedItems.add(ib.getName());
                                    itemdata.put(ib.getId() + "_" + (i + 1), idb.getValue());
                                } else {
                                    String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                                    updateFailedItems.add(key);
                                }
                            }
                            if (err.length() > 0) {
                                String key = i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
                                errors.add("Item " + key + " contains calculation errors: " + err.toString());
                            }
                        }
                    }
                }
            }
        }
        List<ItemFormMetadataBean> itemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(ecb.getCRFVersionId(), ResponseType.GROUP_CALCULATION.getId());
        if (itemList.size() > 0) {
            Collections.sort(itemList);
            for (ItemFormMetadataBean ifmb : itemList) {
                if (ifmb.getSectionId() != sectionId) {
                    ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
                    ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
                    String value = "";
                    Parser p = new Parser(items, itemdata);
                    ArrayList<ScoreToken> parsedExp = parser.parseScoreTokens(rob.getValue());
                    if (p.isChanged(changedItems, parsedExp)) {
                        StringBuffer err = new StringBuffer();
                        parser.setErrors(err);
                        parsedExp = parser.assignVariables(parsedExp, itemOrdinals);
                        ItemDataBean idb = iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), 1);
                        if (parser.getErrors().length() > 0) {
                            err.append(parser.getErrors());
                            if (idb.isActive()) {
                                idb.setValue("<erased>");
                                idb.setStatus(Status.UNAVAILABLE);
                                idb = (ItemDataBean) iddao.update(idb);
                                if (!idb.isActive()) {
                                    updateFailedItems.add(ifmb.getLeftItemText());
                                }
                            }
                        } else {
                            try {
                                value = ScoreUtil.eval(parsedExp);
                            } catch (ScoreException se) {
                                logger.error(se.getMessage());
                            }
                            String exp = rob.getValue();
                            exp = exp.replace("##", ",");
                            if (writeToDB(ib, ifmb, idb, exp, value, err)) {
                                changedItems.add(ib.getName());
                                itemdata.put(ib.getId() + "_" + idb.getOrdinal(), idb.getValue());
                            } else {
                                updateFailedItems.add(ifmb.getLeftItemText());
                            }
                        }
                        if (err.length() > 0) {
                            errors.add("Item " + ifmb.getLeftItemText() + " contains calculation errors: " + err.toString());
                        }
                    }
                }
            }
        }
    } catch (OpenClinicaException e) {
        logger.error(e.getMessage());
    }
    return updateFailedItems;
}

Example 2 with ScoreException

use of org.akaza.openclinica.exception.ScoreException in project OpenClinica by OpenClinica.

the class ScoreUtil method eval.

/**
     * Evaluation math expression which might contain functions.
     * <p>
     * Some pre-conditions:
     * <ul>
     * <li>Supported operators include only '+', '-', '*', '/'
     * <li>Math expression should pass ScoreValidator before evaluation.
     * </ul>
     * 
     * @param expression
     * @return String
     */
public static String eval(ArrayList<ScoreToken> expression) throws ScoreException {
    if (expression == null || expression.size() < 1) {
        return "";
    }
    ScoreToken token = new ScoreToken();
    ArrayList<ScoreToken> finalexp = new ArrayList<ScoreToken>();
    String value = "";
    Info info = new Info();
    info.pos = 0;
    info.level = 0;
    boolean couldBeSign = true;
    while (info.pos < expression.size()) {
        ScoreToken t = new ScoreToken();
        t = expression.get(info.pos);
        char c = t.getSymbol();
        // ignore spaces
        if (c == ' ') {
        // do nothing
        } else if (c == ScoreSymbol.ARITHMETIC_OPERATOR_SYMBOL) {
            if (couldBeSign & isSign(t.getName())) {
                if (token.getName().length() > 0) {
                    logger.info("Wrong at operator " + t.getName() + " at position " + info.pos);
                    throw new ScoreException(t.getName() + " at position " + info.pos + " is invalid.", "1");
                } else {
                    token.setName(t.getName());
                    token.setSymbol(t.getSymbol());
                }
                couldBeSign = false;
            } else {
                if (token.getName().length() > 0) {
                    finalexp.add(token);
                    token = new ScoreToken();
                }
                finalexp.add(t);
                couldBeSign = true;
            }
        } else if (c == '(') {
            couldBeSign = true;
            String sign = "";
            String tokenname = token.getName();
            if (tokenname.length() > 0 && isSign(tokenname.charAt(0))) {
                sign = tokenname.charAt(0) + "";
                tokenname = tokenname.substring(1);
            }
            String funcname = getFunctionName(tokenname);
            if (funcname != null && !funcname.equalsIgnoreCase("getexternalvalue") && !funcname.equalsIgnoreCase(FUNCTION_PACKAGE + "getexternalvalue")) {
                try {
                    token.setName(sign + evalFunc(expression, info, (Function) Class.forName(funcname).newInstance()));
                    token.setSymbol(ScoreSymbol.TERM_SYMBOL);
                } catch (InstantiationException e) {
                    e.printStackTrace();
                } catch (ClassNotFoundException e) {
                    e.printStackTrace();
                } catch (IllegalAccessException e) {
                    e.printStackTrace();
                }
                finalexp.add(token);
                token = new ScoreToken();
                couldBeSign = false;
            } else {
                info.level++;
                if (token.getName().length() > 0) {
                    finalexp.add(token);
                }
                token = new ScoreToken();
                finalexp.add(t);
            }
        } else if (c == ')') {
            couldBeSign = false;
            if (token.getName().length() > 0) {
                finalexp.add(token);
            }
            token = new ScoreToken();
            finalexp.add(t);
            info.level--;
        } else // problem.
        if (c == ',') {
            token = new ScoreToken();
            throw new ScoreException("Found unexpected character , when doing evaluation", "2");
        } else {
            couldBeSign = false;
            if (isSign(token.getName())) {
                token.setName(token.getName() + t.getName());
                token.setSymbol(ScoreSymbol.TERM_SYMBOL);
            } else {
                token.setName(t.getName());
                token.setSymbol(t.getSymbol());
            }
        }
        info.pos++;
    }
    if (info.level != 0) {
        // !!!!!
        logger.info("expression invalid, unpaired parentheses.");
        throw new ScoreException("Found unpaired parentheses when doing evaluation", "3");
    }
    // For example, to expression 2+4, we must do so.
    if (token.getName().length() > 0) {
        finalexp.add(token);
    }
    if (finalexp != null && finalexp.size() > 0) {
        if (finalexp.size() == 1) {
            value = finalexp.get(0).getName();
        } else {
            value = evalSimple(createPostfix(finalexp));
        }
    }
    return "" + value;
}

Example 3 with ScoreException

use of org.akaza.openclinica.exception.ScoreException in project OpenClinica by OpenClinica.

the class ScoreUtil method evalFunc.

/**
     * Evaluate a function which might contain arithmetic expressions, and
     * return result as a String.
     * <p>
     * If an item can not be found in the eventCRF, it will be treated as empty.
     * If empty items exist in a function, the result will be empty.
     * 
     * @param contents
     * @param info
     * @param function
     * @return
     */
public static String evalFunc(ArrayList<ScoreToken> contents, Info info, Function function) throws ScoreException {
    int originalLevel = info.level;
    info.pos++;
    info.level++;
    ScoreToken token = new ScoreToken();
    // currArg is in fact representing the current argument.
    ArrayList<ScoreToken> currArg = new ArrayList<ScoreToken>();
    boolean couldBeSign = true;
    while (info.pos < contents.size()) {
        ScoreToken scoretoken = contents.get(info.pos);
        char c = scoretoken.getSymbol();
        if (c == ')') {
            couldBeSign = false;
            info.level--;
            // end of the function, marked by the equal level
            if (info.level == originalLevel) {
                if (token.getName().length() > 0) {
                    currArg.add(token);
                }
                String t = evalArgument(currArg);
                if (t != null && t.length() > 0) {
                    function.addArgument(t);
                } else {
                    // error message has been handled in evalArgument()
                    return "";
                }
                token = new ScoreToken();
                break;
            } else {
                // argument
                if (token.getName().length() > 0) {
                    currArg.add(token);
                }
                currArg.add(scoretoken);
            }
            token = new ScoreToken();
        } else if (c == '(') {
            couldBeSign = true;
            String sign = "";
            String tokenname = token.getName();
            if (tokenname.length() > 0 && isSign(tokenname.charAt(0))) {
                sign = tokenname.charAt(0) + "";
                tokenname = tokenname.substring(1);
            }
            // it is either the start of a function or an expression
            String funcname = getFunctionName(tokenname);
            if (funcname != null) {
                // store in the current argument
                try {
                    token.setName(sign + evalFunc(contents, info, (Function) Class.forName(funcname).newInstance()));
                    token.setSymbol(ScoreSymbol.TERM_SYMBOL);
                    currArg.add(token);
                    couldBeSign = false;
                } catch (InstantiationException e) {
                    e.printStackTrace();
                    return "";
                } catch (ClassNotFoundException e) {
                    e.printStackTrace();
                    return "";
                } catch (IllegalAccessException e) {
                    e.printStackTrace();
                    return "";
                }
            } else // if it is the start of an expression
            {
                info.level++;
                if (token.getName().length() > 0) {
                    currArg.add(token);
                }
                currArg.add(scoretoken);
            }
            token = new ScoreToken();
        } else // end of an argument
        if (c == ',') {
            couldBeSign = true;
            if (token.getName().length() > 0) {
                currArg.add(token);
            }
            // compute the argument
            String t = evalArgument(currArg);
            if (t != null && t.length() > 0) {
                function.addArgument(t);
            } else {
                return "";
            }
            token = new ScoreToken();
            // reset the argument for next one
            currArg = new ArrayList<ScoreToken>();
        } else // else if(isOperator(c)){
        if (c == ScoreSymbol.ARITHMETIC_OPERATOR_SYMBOL) {
            if (couldBeSign && isSign(scoretoken.getName())) {
                if (token.getName().length() > 0) {
                    throw new ScoreException(scoretoken.getName() + " at position " + info.pos + " is invalid.", "1");
                } else {
                    // token = scoretoken;
                    token.setName(scoretoken.getName());
                    token.setSymbol(scoretoken.getSymbol());
                }
                couldBeSign = false;
            } else {
                if (token.getName().length() > 0) {
                    currArg.add(token);
                }
                token = new ScoreToken();
                currArg.add(scoretoken);
                couldBeSign = true;
            }
        } else {
            couldBeSign = false;
            if (isSign(token.getName())) {
                token.setName(token.getName() + scoretoken.getName());
                token.setSymbol(ScoreSymbol.TERM_SYMBOL);
            } else {
                if (c != ' ') {
                    // token = scoretoken;
                    token.setName(scoretoken.getName());
                    token.setSymbol(scoretoken.getSymbol());
                }
            }
        }
        info.pos++;
    }
    function.execute();
    if (function.getErrors().size() > 0) {
        String errors = new String();
        HashMap<Integer, String> es = function.getErrors();
        for (int i = 0; i < es.size(); ++i) {
            errors += es.get(Integer.valueOf(i));
        }
        throw new ScoreException(errors, "4");
    }
    return function.getValue();
}

Example 4 with ScoreException

use of org.akaza.openclinica.exception.ScoreException in project OpenClinica by OpenClinica.

the class ScoreCalculator method doCalculation.

/*
     * Perform all calculations in a CRFVersion. The parameter 'itemdata' might
     * be overwritten.
     * 
     * @param calcItemGroupSizes @param items @param itemdata @param
     * itemGroupSizes @param databaseErrors @return ArrayList<String> which
     * records left_item_text of items who failed to be updated into database.
     * 
     * 
     * //this method has not been fully tested yet
     * 
     * 
     * public ArrayList<String> doCalculations( HashMap<String,ItemBean>
     * items, HashMap<String,String> itemdata, HashMap<Integer,TreeSet<Integer>>
     * itemOrdinals) { ArrayList<String> updateFailedItems = new ArrayList<String>();
     * if(itemdata==null) { //here, actually only record errors but doesn't
     * return errors. logger.error("In scoreCalculator doCalculations(), items
     * are empty!"); errors.add("Calculation cannot be started because needed
     * items are empty!"); return updateFailedItems; } ItemFormMetadataDAO
     * ifmdao = new ItemFormMetadataDAO(sm.getDataSource()); ItemDAO idao = new
     * ItemDAO(sm.getDataSource()); ItemDataDAO iddao = new
     * ItemDataDAO(sm.getDataSource());
     * 
     * NumberFormat nf = NumberFormat.getInstance(); Parser parser = new
     * Parser(items,itemdata); try { //for calculation type List<ItemFormMetadataBean>
     * derivedItemList = ifmdao.findAllByCRFVersionIdAndResponseTypeId(
     * ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
     * if(derivedItemList.size()>0) { Collections.sort(derivedItemList); for
     * (ItemFormMetadataBean ifmb: derivedItemList) { ItemBean ib =
     * (ItemBean)idao.findByPK(ifmb.getItemId()); ResponseOptionBean rob =
     * (ResponseOptionBean)ifmb.getResponseSet().getOptions().get(0); //YW,
     * 1-16-2008, << enable: 1. evaluate combination of expression and
     * functions 2. scoring for group items. //int groupsize =
     * iddao.getMaxOrdinalForGroup(ecb,
     * (SectionBean)sdao.findByPK(ifmb.getSectionId()), //
     * (ItemGroupBean)igdao.findByName(ifmb.getGroupLabel())); int groupsize =
     * 1; if(itemOrdinals.containsKey(ib.getId())) { groupsize =
     * (itemOrdinals.get(ib.getId())).size(); } String value = ""; String
     * parsedExp = ""; for(int i=0; i<groupsize; ++i) { ItemDataBean idb =
     * (ItemDataBean)iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb
     * .getItemId(), ecb.getId(), i+1); StringBuffer err = new StringBuffer();
     * parsedExp = parser.parse(rob.getValue(), i+1);
     * if(parser.getErrors().length()>0) { err.append(parser.getErrors());
     * parser.setErrors(new StringBuffer()); } else { value =
     * ScoreUtil.eval(parsedExp, err); //YW >> String exp = rob.getValue(); exp =
     * exp.replace("##", ","); if(writeToDB(ib,idb,exp,value,err)) {
     * itemdata.put(ib.getId()+"_"+(i+1), idb.getValue()); }else { String key =
     * (i+1)>1 ? ifmb.getLeftItemText()+"_"+(i+1) : ifmb.getLeftItemText();
     * updateFailedItems.add(key); } } if(err.length()>0) { String key = (i+1)>1 ?
     * ifmb.getLeftItemText()+"_"+(i+1) : ifmb.getLeftItemText();
     * errors.add("Item " + key + " contains calculation errors: " +
     * err.toString()); } } } }
     * 
     * //YW, 1-16-2008, for group-calculation type. Current restrictions: //1.
     * an item with group-calculation type is not repeatable. //2. only
     * calculate sum(), avg(), min(), max(), median(), stdev() //3. formula
     * arguments only contain item beans //4. only one item bean per argument
     * List<ItemFormMetadataBean> itemList =
     * ifmdao.findAllByCRFVersionIdAndResponseTypeId( ecb.getCRFVersionId(),
     * ResponseType.GROUP_CALCULATION.getId()); if(itemList.size()>0) {
     * Collections.sort(itemList); for (ItemFormMetadataBean ifmb: itemList) {
     * ItemBean ib = (ItemBean)idao.findByPK(ifmb.getItemId());
     * ResponseOptionBean rob =
     * (ResponseOptionBean)ifmb.getResponseSet().getOptions().get(0);
     * StringBuffer err = new StringBuffer(); parser.setErrors(err); String
     * parsedExp = parser.parse(rob.getValue(),itemOrdinals); String value = "";
     * if(parser.getErrors().length()>0) { err.append(parser.getErrors()); }else {
     * value = ScoreUtil.eval(parsedExp,err);
     * 
     * ItemDataBean idb =
     * (ItemDataBean)iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb
     * .getItemId(), ecb.getId(), 1); String exp = rob.getValue(); exp =
     * exp.replace("##", ","); if(writeToDB(ib,idb,exp,value,err)) {
     * itemdata.put(ib.getId()+"_"+idb.getOrdinal(), idb.getValue()); } else {
     * updateFailedItems.add(ifmb.getLeftItemText()); } }
     * 
     * if(err.length()>0) { errors.add("Item " + ifmb.getLeftItemText() + "
     * contains calculation errors: " + err.toString()); } } } } catch
     * (OpenClinicaException e) { logger.error(e.getMessage()); }
     * //ecb.setNeedsRecalc(false); //EventCRFDAO ecdao = new
     * EventCRFDAO(sm.getDataSource()); //ecb = ecdao.update(ecb);
     * 
     * return updateFailedItems; }
     */
/**
     * Performs calculation. <br>
     * Notice: both parameter 'itemdata' and parameter 'errs' might be updated
     * in this method.
     * 
     * @param displayItems
     * @param items
     * @param itemdata
     * @param errs
     * @return
     * 
     * @author ywang (Jan. 2008)
     */
public String doCalculation(DisplayItemBean displayItem, HashMap<String, ItemBean> items, HashMap<String, String> itemdata, HashMap<Integer, TreeSet<Integer>> itemOrdinals, StringBuffer errs, int ordinal) {
    if (itemdata == null) {
        logger.error("In DataEntryServlet doCalculation(), itemdata map is empty!");
        errs.append("Calculation cannot be started because needed items are empty" + "; ");
        return "";
    }
    String value = "";
    NumberFormat nf = NumberFormat.getInstance();
    Parser parser = new Parser(items, itemdata);
    ItemBean ib = displayItem.getItem();
    ItemFormMetadataBean ifm = displayItem.getMetadata();
    ResponseOptionBean rob = (ResponseOptionBean) ifm.getResponseSet().getOptions().get(0);
    ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
    int type = ifm.getResponseSet().getResponseTypeId();
    if (type == 8) {
        parsedExp = parser.assignVariables(parser.parseScoreTokens(rob.getValue()), ordinal);
    } else if (type == 9) {
        // YW, 1-16-2008, for group-calculation type. Current restrictions:
        // 1. only calculate sum(), avg(), min(), max(), median(), stdev()
        // 2. formula arguments only contain item beans
        // 3. only one item bean per argument
        parsedExp = parser.assignVariables(parser.parseScoreTokens(rob.getValue()), itemOrdinals);
    }
    if (parser.getErrors().length() > 0) {
        errs.append(parser.getErrors());
    } else {
        try {
            value = ScoreUtil.eval(parsedExp);
        } catch (ScoreException se) {
            logger.error(se.getMessage());
        }
        ItemDataType idt = ib.getDataType();
        if (value == null || value.length() == 0) {
            value = "";
            String exp = rob.getValue();
            exp = exp.replace("##", ",");
            errs.append("Result is empty in" + " " + exp + "; ");
        // errors.append(resexception.getString("result_is_empty_in") +
        // " " + exp + "; ");
        } else {
            value = this.getMathContextValue(value, ifm, idt, errs);
        }
        // idb.setStatus(Status.UNAVAILABLE);
        itemdata.put(ib.getId() + "_" + ordinal, value);
    }
    return value;
}