Examples with ItemBean org.akaza.openclinica.bean.submit.ItemBean used on opensource projects

Example 71 with ItemBean

use of org.akaza.openclinica.bean.submit.ItemBean in project OpenClinica by OpenClinica.

the class ItemDAO method findByNameAndCRFId.

public EntityBean findByNameAndCRFId(String name, int crfId) {
    ItemBean eb = new ItemBean();
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), name);
    variables.put(new Integer(2), new Integer(crfId));
    String sql = digester.getQuery("findByNameAndCRFId");
    ArrayList alist = this.select(sql, variables);
    Iterator it = alist.iterator();
    if (it.hasNext()) {
        eb = (ItemBean) this.getEntityFromHashMap((HashMap) it.next());
    }
    return eb;
}

Example 72 with ItemBean

use of org.akaza.openclinica.bean.submit.ItemBean in project OpenClinica by OpenClinica.

the class ItemDAO method findAllItemsByGroupIdOrdered.

public List<ItemBean> findAllItemsByGroupIdOrdered(int id, int crfVersionId) {
    this.setTypesExpected();
    HashMap<Integer, Integer> variables = new HashMap<Integer, Integer>();
    variables.put(1, id);
    variables.put(2, crfVersionId);
    String sql = digester.getQuery("findAllItemsByGroupIdOrdered");
    List listofMaps = this.select(sql, variables);
    List<ItemBean> beanList = new ArrayList<ItemBean>();
    ItemBean bean;
    for (Object map : listofMaps) {
        bean = (ItemBean) this.getEntityFromHashMap((HashMap) map);
        beanList.add(bean);
    }
    return beanList;
}

Example 73 with ItemBean

use of org.akaza.openclinica.bean.submit.ItemBean 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;
}

Example 74 with ItemBean

use of org.akaza.openclinica.bean.submit.ItemBean in project OpenClinica by OpenClinica.

the class SPSSReportBean method getMetadataFile.

public StringBuffer getMetadataFile(SPSSVariableNameValidator svnv, ExtractBean eb) {
    itemNames.clear();
    // Is it necessary to
    String[] attributes = createAttributes(eb);
    // validate
    // StudyGroupClassBean
    // names? YW
    String[] attributeTypes = createAttributeTypes(eb);
    StringBuffer answer = new StringBuffer();
    answer.append("* NOTE: If you have put this file in a different folder \n" + "* from the associated data file, you will have to change the FILE \n" + "* location on the line below to point to the physical location of your data file.\n");
    answer.append("GET DATA  " + "/TYPE = TXT" + "/FILE = '" + getDatFileName() + "' " + "/DELCASE = LINE " + "/DELIMITERS = \"\\t\" " + "/ARRANGEMENT = DELIMITED " + "/FIRSTCASE = " + FIRSTCASE + " " + // since
    "/IMPORTCASE = ALL ");
    if (data.size() <= 0) {
        answer.append(".\n");
    } else {
        ArrayList columns = (ArrayList) data.get(this.COLUMNS_IND);
        int startItem = columns.size() - items.size();
        logger.debug("--> generated start item " + startItem + " from " + columns.size() + " minus " + items.size());
        answer.append("/VARIABLES = \n");
        int index;
        for (int i = 0; i < columns.size(); i++) {
            String itemName = (String) columns.get(i);
            // YW << Why do we need "V_" here? Right now it has been
            // removed, because:
            // This "V_" exists in .sps file but not exists in .dat file.
            // String varLabel = "V_" + itemName;
            String varLabel = svnv.getValidName(itemName);
            itemNames.add(varLabel);
            // builtin attributes
            if (i < startItem) {
                if (varLabel.startsWith("Gender")) {
                    gender = true;
                }
                index = builtinIndex(varLabel, attributes);
                logger.debug("varLabel[" + varLabel + "] index[" + index + "] attributeTypes[" + attributeTypes[1] + "]");
                answer.append("\t" + varLabel + " " + attributeTypes[index]);
                // >> tbh #5524
                DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i);
                ItemBean ib = dih.getItem();
                // << tbh
                if (attributeTypes[index].equals("A")) {
                    int len = getDataColumnMaxLen(i);
                    if (len == 0) {
                        // mininum length required by spss
                        len = 1;
                    }
                    // >> tbh #5524
                    ArrayList metas = ib.getItemMetas();
                    for (int k = 0; k < metas.size(); k++) {
                        ItemFormMetadataBean ifmb = (ItemFormMetadataBean) metas.get(k);
                        ResponseSetBean rsb = ifmb.getResponseSet();
                        ArrayList options = rsb.getOptions();
                        for (int l = 0; l < options.size(); l++) {
                            ResponseOptionBean ro = (ResponseOptionBean) options.get(l);
                            if (ro.getText().length() > len) {
                                len = ro.getText().length();
                            }
                        }
                    }
                    // << tbh
                    if (len > 8) {
                        len = 8;
                    }
                    answer.append(len);
                }
                answer.append("\n");
            }
        // YW >>
        }
        // items
        logger.debug("--> looking at " + startItem + " out of " + columns.size());
        for (int i = startItem; i < columns.size(); i++) {
            DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i - startItem);
            ItemBean ib = dih.getItem();
            // YW <<
            String varLabel = (String) itemNames.get(i);
            int dataTypeId = ib.getItemDataTypeId();
            // String.
            if (dataTypeId == 9) {
                // date
                answer.append("\t" + varLabel + " ADATE10\n");
            } else if (dataTypeId == 7) {
                // float
                answer.append("\t" + varLabel + " F8.2\n");
            } else if (dataTypeId == 6 && isIntType(ib)) {
                // pure int data
                // type for one
                // item.
                answer.append("\t" + varLabel + " F8.0\n");
            } else {
                // string
                // YW >>
                int len = getDataColumnMaxLen(i);
                if (len == 0) {
                    // mininum length required by spss
                    len = 1;
                }
                ArrayList metas = ib.getItemMetas();
                int optionCount = 0;
                for (int k = 0; k < metas.size(); k++) {
                    ItemFormMetadataBean ifmb = (ItemFormMetadataBean) metas.get(k);
                    ResponseSetBean rsb = ifmb.getResponseSet();
                    if (rsb.getResponseType().equals(ResponseType.CHECKBOX) || rsb.getResponseType().equals(ResponseType.RADIO) || rsb.getResponseType().equals(ResponseType.SELECT) || rsb.getResponseType().equals(ResponseType.SELECTMULTI)) {
                        optionCount++;
                    }
                    // tbh >> #5524: all possible response value options should be reviewed so that length is OK
                    ArrayList options = rsb.getOptions();
                    for (int l = 0; l < options.size(); l++) {
                        ResponseOptionBean ro = (ResponseOptionBean) options.get(l);
                        if (ro.getText().length() > len) {
                            len = ro.getText().length();
                        }
                    }
                // << tbh
                }
                if (optionCount == metas.size()) {
                    // value labels
                    if (len > 8) {
                        len = 8;
                    }
                }
                answer.append("\t" + varLabel + " A" + len + "\n");
            }
        }
        answer.append(".\n");
        answer.append("VARIABLE LABELS\n");
        // builtin attributes
        for (int i = 0; i < startItem; ++i) {
            String varLabel = (String) itemNames.get(i);
            if ((String) descriptions.get(itemNames.get(i)) != null) {
                answer.append("\t" + varLabel + " \"" + (String) descriptions.get(itemNames.get(i)) + "\"\n");
            } else {
                for (int j = 0; j < eb.getStudyGroupClasses().size(); ++j) {
                    answer.append("\t" + varLabel + " \"" + (String) descriptions.get(((StudyGroupClassBean) eb.getStudyGroupClasses().get(j)).getName()) + "\"\n");
                }
            }
        }
        // items
        for (int i = startItem; i < itemNames.size(); i++) {
            DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i - startItem);
            ItemBean ib = dih.getItem();
            String varLabel = (String) itemNames.get(i);
            answer.append("\t" + varLabel + " \"" + ib.getDescription() + "\"\n");
        }
        answer.append(".\n");
        answer.append("VALUE LABELS\n");
        if (isGender()) {
            answer.append("\t" + "Gender" + "\n");
            answer.append("\t" + "'M'" + " \"" + "Male" + "\"\n");
            answer.append("\t" + "'F'" + " \"" + "Female" + "\"\n\t/\n");
        }
        for (int i = 0; i < items.size(); i++) {
            String temp = "";
            DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i);
            ItemBean ib = dih.getItem();
            String varLabel = (String) itemNames.get(i + startItem);
            temp += "\t" + varLabel + "\n";
            boolean allOption = true;
            ArrayList metas = ib.getItemMetas();
            HashMap optionMap = new LinkedHashMap();
            for (int k = 0; k < metas.size(); k++) {
                ItemFormMetadataBean ifmb = (ItemFormMetadataBean) metas.get(k);
                ResponseSetBean rsb = ifmb.getResponseSet();
                if (rsb.getResponseType().equals(ResponseType.TEXT) || rsb.getResponseType().equals(ResponseType.FILE) || rsb.getResponseType().equals(ResponseType.TEXTAREA)) {
                    // has text response, dont show value labels
                    allOption = false;
                    break;
                } else {
                    for (int j = 0; j < rsb.getOptions().size(); j++) {
                        ResponseOptionBean ob = (ResponseOptionBean) rsb.getOptions().get(j);
                        String key = ob.getValue();
                        if (optionMap.containsKey(key)) {
                            ArrayList a = (ArrayList) optionMap.get(key);
                            if (!a.contains(ob.getText())) {
                                a.add(ob.getText());
                                optionMap.put(key, a);
                            }
                        } else {
                            ArrayList a = new ArrayList();
                            a.add(ob.getText());
                            optionMap.put(key, a);
                        }
                    }
                }
            }
            Iterator it = optionMap.keySet().iterator();
            while (it.hasNext()) {
                String value = (String) it.next();
                ArrayList a = (ArrayList) optionMap.get(value);
                String texts = "";
                if (a.size() > 1) {
                    for (int n = 0; n < a.size(); n++) {
                        texts += (String) a.get(n);
                        if (n < a.size() - 1) {
                            texts += "/";
                        }
                    }
                } else {
                    texts = (String) a.get(0);
                }
                if (value.length() > 8) {
                    value = value.substring(0, 8);
                }
                if (isValueText(value)) {
                    temp += "\t'" + value + "' \"" + texts + "\"\n";
                } else {
                    temp += "\t" + value + " \"" + texts + "\"\n";
                }
            }
            if (allOption) {
                answer.append(temp + "\t/\n");
            }
        }
    }
    answer.append(".\n EXECUTE.\n");
    return answer;
}

Example 75 with ItemBean

use of org.akaza.openclinica.bean.submit.ItemBean in project OpenClinica by OpenClinica.

the class ItemDAO method findAllWithItemDataByFormLayoutId.

// select name, ordinal, oc_oid, item_data_id, i.item_id as item_id, value
//
// from item_data id, item i
// where id.item_id=i.item_id and event_crf_id = ? order by i.item_id,ordinal;
public ArrayList<ItemBean> findAllWithItemDataByFormLayoutId(int crfVersionId, int eventCRFId) {
    this.unsetTypeExpected();
    // (item)name
    this.setTypeExpected(1, TypeNames.STRING);
    // ordinal
    this.setTypeExpected(2, TypeNames.INT);
    // oc_oid
    this.setTypeExpected(3, TypeNames.STRING);
    // item_data_id
    this.setTypeExpected(4, TypeNames.INT);
    // item_id
    this.setTypeExpected(5, TypeNames.INT);
    // (item)value
    this.setTypeExpected(6, TypeNames.STRING);
    ArrayList<ItemBean> answer = new ArrayList<ItemBean>();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), new Integer(crfVersionId));
    variables.put(new Integer(2), new Integer(eventCRFId));
    String sql = digester.getQuery("findAllWithItemDataByFormLayoutId");
    ArrayList rows = super.select(sql, variables);
    Iterator it = rows.iterator();
    int cur_item_id = 0;
    ItemBean item_bean = null;
    ItemDataBean item_data_bean = null;
    while (it.hasNext()) {
        HashMap row = (HashMap) it.next();
        Integer id = (Integer) row.get("item_id");
        if (cur_item_id != id.intValue()) {
            item_bean = new ItemBean();
            answer.add(item_bean);
            cur_item_id = id.intValue();
            item_bean.setId(cur_item_id);
            item_bean.setName((String) row.get("name"));
            item_bean.setOid((String) row.get("oc_oid"));
        }
        item_data_bean = new ItemDataBean();
        item_data_bean.setValue((String) row.get("value"));
        item_data_bean.setOrdinal(((Integer) row.get("ordinal")).intValue());
        item_data_bean.setId(((Integer) row.get("item_data_id")).intValue());
        item_data_bean.setItemId(cur_item_id);
        item_bean.addItemDataElement(item_data_bean);
    }
    return answer;
}