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

Example 51 with OpenClinicaSystemException

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

the class CoreResources method copyBaseToDest.

private void copyBaseToDest(ResourceLoader resourceLoader) {
    ResourcePatternResolver resolver = new PathMatchingResourcePatternResolver(resourceLoader);
    Resource[] resources;
    try {
        /*
             * Use classpath* to search for resources that match this pattern in ALL of the jars in the application
             * class path. See:
             * http://static.springsource.org/spring/docs/3.0.x/spring-framework-reference/html/resources
             * .html#resources-classpath-wildcards
             */
        resources = resolver.getResources("classpath*:properties/xslt/*.xsl");
    } catch (IOException ioe) {
        logger.debug(ioe.getMessage(), ioe);
        throw new OpenClinicaSystemException("Unable to read source files", ioe);
    }
    File dest = new File(getField("filePath") + "xslt");
    if (!dest.exists()) {
        if (!dest.mkdirs()) {
            throw new OpenClinicaSystemException("Copying files, Could not create direcotry: " + dest.getAbsolutePath() + ".");
        }
    }
    for (Resource r : resources) {
        File f = new File(dest, r.getFilename());
        try {
            FileOutputStream out = new FileOutputStream(f);
            IOUtils.copy(r.getInputStream(), out);
            out.close();
        } catch (IOException ioe) {
            logger.debug(ioe.getMessage(), ioe);
            throw new OpenClinicaSystemException("Unable to copy file: " + r.getFilename() + " to " + f.getAbsolutePath(), ioe);
        }
    }
}

Example 52 with OpenClinicaSystemException

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

the class CoreResources method checkForFile.

private void checkForFile(String[] extractFields) throws OpenClinicaSystemException {
    int cnt = extractFields.length;
    int i = 0;
    // iterate through all comma separated file names
    while (i < cnt) {
        File f = new File(getField("filePath") + "xslt" + File.separator + extractFields[i]);
        // System.out.println(getField("filePath") + "xslt" + File.separator + extractFields[i]);
        if (!f.exists())
            throw new OpenClinicaSystemException("FileNotFound -- Please make sure" + extractFields[i] + "exists");
        i++;
    }
}

Example 53 with OpenClinicaSystemException

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

the class Key method runRulesBulk.

public HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>> runRulesBulk(List<RuleSetBean> ruleSets, ExecutionMode executionMode, StudyBean currentStudy, HashMap<String, String> variableAndValue, UserAccountBean ub) {
    if (variableAndValue == null || variableAndValue.isEmpty()) {
        logger.warn("You must be executing Rules in Batch");
        variableAndValue = new HashMap<String, String>();
    }
    HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>> crfViewSpecificOrderedObjects = new HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>>();
    HashMap<String, ArrayList<RuleActionContainer>> toBeExecuted = new HashMap<String, ArrayList<RuleActionContainer>>();
    for (RuleSetBean ruleSet : ruleSets) {
        String key = getExpressionService().getItemOid(ruleSet.getOriginalTarget().getValue());
        List<RuleActionContainer> allActionContainerListBasedOnRuleExecutionResult = null;
        if (toBeExecuted.containsKey(key)) {
            allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
        } else {
            toBeExecuted.put(key, new ArrayList<RuleActionContainer>());
            allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
        }
        ItemDataBean itemData = null;
        for (ExpressionBean expressionBean : ruleSet.getExpressions()) {
            ruleSet.setTarget(expressionBean);
            for (RuleSetRuleBean ruleSetRule : ruleSet.getRuleSetRules()) {
                String result = null;
                RuleBean rule = ruleSetRule.getRuleBean();
                ExpressionObjectWrapper eow = new ExpressionObjectWrapper(ds, currentStudy, rule.getExpression(), ruleSet, variableAndValue);
                try {
                    OpenClinicaExpressionParser oep = new OpenClinicaExpressionParser(eow);
                    result = (String) oep.parseAndEvaluateExpression(rule.getExpression().getValue());
                    itemData = getExpressionService().getItemDataBeanFromDb(ruleSet.getTarget().getValue());
                    // Actions
                    List<RuleActionBean> actionListBasedOnRuleExecutionResult = ruleSetRule.getActions(result, Phase.BATCH);
                    if (itemData != null) {
                        Iterator<RuleActionBean> itr = actionListBasedOnRuleExecutionResult.iterator();
                        while (itr.hasNext()) {
                            RuleActionBean ruleActionBean = itr.next();
                            RuleActionRunLogBean ruleActionRunLog = new RuleActionRunLogBean(ruleActionBean.getActionType(), itemData, itemData.getValue(), ruleSetRule.getRuleBean().getOid());
                            if (getRuleActionRunLogDao().findCountByRuleActionRunLogBean(ruleActionRunLog) > 0) {
                                itr.remove();
                            }
                        }
                    }
                    for (RuleActionBean ruleActionBean : actionListBasedOnRuleExecutionResult) {
                        RuleActionContainer ruleActionContainer = new RuleActionContainer(ruleActionBean, expressionBean, itemData, ruleSet);
                        allActionContainerListBasedOnRuleExecutionResult.add(ruleActionContainer);
                    }
                    logger.info("RuleSet with target  : {} , Ran Rule : {}  The Result was : {} , Based on that {} action will be executed in {} mode. ", new Object[] { ruleSet.getTarget().getValue(), rule.getName(), result, actionListBasedOnRuleExecutionResult.size(), executionMode.name() });
                } catch (OpenClinicaSystemException osa) {
                // TODO: report something useful 
                }
            }
        }
    }
    for (Map.Entry<String, ArrayList<RuleActionContainer>> entry : toBeExecuted.entrySet()) {
        // Sort the list of actions
        Collections.sort(entry.getValue(), new RuleActionContainerComparator());
        HashMap<Key, List<RuleActionBean>> hms = new HashMap<Key, List<RuleActionBean>>();
        for (RuleActionContainer ruleActionContainer : entry.getValue()) {
            //ruleSet.setTarget(ruleAction.getRuleSetExpression());
            ruleActionContainer.getRuleAction().setCuratedMessage(curateMessage(ruleActionContainer.getRuleAction(), ruleActionContainer.getRuleAction().getRuleSetRule()));
            ActionProcessor ap = ActionProcessorFacade.getActionProcessor(ruleActionContainer.getRuleAction().getActionType(), ds, getMailSender(), dynamicsMetadataService, ruleActionContainer.getRuleSetBean(), getRuleActionRunLogDao(), ruleActionContainer.getRuleAction().getRuleSetRule());
            RuleActionBean rab = null;
            ap.execute(RuleRunnerMode.RULSET_BULK, executionMode, ruleActionContainer.getRuleAction(), ruleActionContainer.getItemDataBean(), DiscrepancyNoteBean.ITEM_DATA, currentStudy, ub, prepareEmailContents(ruleActionContainer.getRuleSetBean(), ruleActionContainer.getRuleAction().getRuleSetRule(), currentStudy, ruleActionContainer.getRuleAction()));
            if (rab != null) {
                Key k = new Key(ruleActionContainer.getRuleSetBean(), ruleActionContainer.getRuleAction().getExpressionEvaluatesTo().toString(), ruleActionContainer.getRuleAction().getRuleSetRule().getRuleBean());
                if (hms.containsKey(k)) {
                    hms.get(k).add(ruleActionContainer.getRuleAction());
                } else {
                    List<RuleActionBean> theActionBeansToShow = new ArrayList<RuleActionBean>();
                    theActionBeansToShow.add(ruleActionContainer.getRuleAction());
                    hms.put(k, theActionBeansToShow);
                }
            }
        }
        for (Map.Entry<Key, List<RuleActionBean>> theEntry : hms.entrySet()) {
            Key key = theEntry.getKey();
            List<RuleActionBean> value = theEntry.getValue();
            crfViewSpecificOrderedObjects = populateForCrfBasedRulesView(crfViewSpecificOrderedObjects, key.getRuleSet(), key.getRule(), key.getResult(), currentStudy, value);
        }
    }
    //logCrfViewSpecificOrderedObjects(crfViewSpecificOrderedObjects);
    return crfViewSpecificOrderedObjects;
}

Example 54 with OpenClinicaSystemException

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

the class DataEntryRuleRunner method runRules.

public MessageContainer runRules(List<RuleSetBean> ruleSets, ExecutionMode executionMode, StudyBean currentStudy, HashMap<String, String> variableAndValue, UserAccountBean ub, Phase phase, HttpServletRequest request) {
    if (variableAndValue == null || variableAndValue.isEmpty()) {
        logger.warn("You must be executing Rules in Batch");
        variableAndValue = new HashMap<String, String>();
    }
    MessageContainer messageContainer = new MessageContainer();
    HashMap<String, ArrayList<RuleActionContainer>> toBeExecuted = new HashMap<String, ArrayList<RuleActionContainer>>();
    switch(executionMode) {
        case SAVE:
            {
                toBeExecuted = (HashMap<String, ArrayList<RuleActionContainer>>) request.getAttribute("toBeExecuted");
                if (//Break only if the action is insertAction;
                request.getAttribute("insertAction") == null) {
                    break;
                } else {
                    toBeExecuted = new HashMap<String, ArrayList<RuleActionContainer>>();
                }
            }
        case DRY_RUN:
            {
                for (RuleSetBean ruleSet : ruleSets) {
                    String key = getExpressionService().getItemOid(ruleSet.getOriginalTarget().getValue());
                    List<RuleActionContainer> allActionContainerListBasedOnRuleExecutionResult = null;
                    if (toBeExecuted.containsKey(key)) {
                        allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
                    } else {
                        toBeExecuted.put(key, new ArrayList<RuleActionContainer>());
                        allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
                    }
                    ItemDataBean itemData = null;
                    for (ExpressionBean expressionBean : ruleSet.getExpressions()) {
                        ruleSet.setTarget(expressionBean);
                        for (RuleSetRuleBean ruleSetRule : ruleSet.getRuleSetRules()) {
                            String result = null;
                            RuleBean rule = ruleSetRule.getRuleBean();
                            ExpressionObjectWrapper eow = new ExpressionObjectWrapper(ds, currentStudy, rule.getExpression(), ruleSet, variableAndValue, ecb);
                            try {
                                OpenClinicaExpressionParser oep = new OpenClinicaExpressionParser(eow);
                                result = (String) oep.parseAndEvaluateExpression(rule.getExpression().getValue());
                                itemData = getExpressionService().getItemDataBeanFromDb(ruleSet.getTarget().getValue());
                                // Actions
                                List<RuleActionBean> actionListBasedOnRuleExecutionResult = ruleSetRule.getActions(result, phase);
                                if (itemData != null) {
                                    Iterator<RuleActionBean> itr = actionListBasedOnRuleExecutionResult.iterator();
                                    String firstDDE = "firstDDEInsert_" + ruleSetRule.getOid() + "_" + itemData.getId();
                                    while (itr.hasNext()) {
                                        RuleActionBean ruleActionBean = itr.next();
                                        if (ruleActionBean.getActionType() == ActionType.INSERT) {
                                            request.setAttribute("insertAction", true);
                                            if (phase == Phase.DOUBLE_DATA_ENTRY && itemData.getStatus().getId() == 4 && request.getAttribute(firstDDE) == null) {
                                                request.setAttribute(firstDDE, true);
                                            }
                                        }
                                        if (request.getAttribute(firstDDE) == Boolean.TRUE) {
                                        } else {
                                            String itemDataValueFromForm = "";
                                            if (variableAndValue.containsKey(key)) {
                                                itemDataValueFromForm = variableAndValue.get(key);
                                            } else {
                                                logger.info("Cannot find value from variableAndValue for item=" + key + ". " + "Used itemData.getValue()");
                                                itemDataValueFromForm = itemData.getValue();
                                            }
                                            RuleActionRunLogBean ruleActionRunLog = new RuleActionRunLogBean(ruleActionBean.getActionType(), itemData, itemDataValueFromForm, ruleSetRule.getRuleBean().getOid());
                                            if (getRuleActionRunLogDao().findCountByRuleActionRunLogBean(ruleActionRunLog) > 0) {
                                                itr.remove();
                                            }
                                        }
                                    }
                                }
                                for (RuleActionBean ruleActionBean : actionListBasedOnRuleExecutionResult) {
                                    RuleActionContainer ruleActionContainer = new RuleActionContainer(ruleActionBean, expressionBean, itemData, ruleSet);
                                    allActionContainerListBasedOnRuleExecutionResult.add(ruleActionContainer);
                                }
                                logger.info("RuleSet with target  : {} , Ran Rule : {}  The Result was : {} , Based on that {} action will be executed in {} mode. ", new Object[] { ruleSet.getTarget().getValue(), rule.getName(), result, actionListBasedOnRuleExecutionResult.size(), executionMode.name() });
                            } catch (OpenClinicaSystemException osa) {
                            // TODO: report something useful 
                            }
                        }
                    }
                }
                request.setAttribute("toBeExecuted", toBeExecuted);
                break;
            }
    }
    for (Map.Entry<String, ArrayList<RuleActionContainer>> entry : toBeExecuted.entrySet()) {
        // Sort the list of actions
        Collections.sort(entry.getValue(), new RuleActionContainerComparator());
        for (RuleActionContainer ruleActionContainer : entry.getValue()) {
            logger.info("START Expression is : {} , RuleAction : {} , ExecutionMode : {} ", new Object[] { ruleActionContainer.getExpressionBean().getValue(), ruleActionContainer.getRuleAction().toString(), executionMode });
            ruleActionContainer.getRuleSetBean().setTarget(ruleActionContainer.getExpressionBean());
            ruleActionContainer.getRuleAction().setCuratedMessage(curateMessage(ruleActionContainer.getRuleAction(), ruleActionContainer.getRuleAction().getRuleSetRule()));
            ActionProcessor ap = ActionProcessorFacade.getActionProcessor(ruleActionContainer.getRuleAction().getActionType(), ds, getMailSender(), dynamicsMetadataService, ruleActionContainer.getRuleSetBean(), getRuleActionRunLogDao(), ruleActionContainer.getRuleAction().getRuleSetRule());
            ItemDataBean itemData = getExpressionService().getItemDataBeanFromDb(ruleActionContainer.getRuleSetBean().getTarget().getValue());
            RuleActionBean rab = ap.execute(RuleRunnerMode.DATA_ENTRY, executionMode, ruleActionContainer.getRuleAction(), itemData, DiscrepancyNoteBean.ITEM_DATA, currentStudy, ub, prepareEmailContents(ruleActionContainer.getRuleSetBean(), ruleActionContainer.getRuleAction().getRuleSetRule(), currentStudy, ruleActionContainer.getRuleAction()));
            if (rab != null) {
                if (rab instanceof ShowActionBean) {
                    messageContainer.add(getExpressionService().getGroupOidOrdinal(ruleActionContainer.getRuleSetBean().getTarget().getValue()), rab);
                } else {
                    messageContainer.add(getExpressionService().getGroupOrdninalConcatWithItemOid(ruleActionContainer.getRuleSetBean().getTarget().getValue()), ruleActionContainer.getRuleAction());
                }
            }
            logger.info("END Expression is : {} , RuleAction : {} , ExecutionMode : {} ", new Object[] { ruleActionContainer.getExpressionBean().getValue(), ruleActionContainer.getRuleAction().toString(), executionMode });
        }
    }
    return messageContainer;
}

Example 55 with OpenClinicaSystemException

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

the class ImportDataRuleRunner method populateToBeExpected.

@Transactional
private HashMap<String, ArrayList<RuleActionContainer>> populateToBeExpected(ImportDataRuleRunnerContainer container, StudyBean study, UserAccountBean ub) {
    //copied code for toBeExpected from DataEntryServlet runRules
    HashMap<String, ArrayList<RuleActionContainer>> toBeExecuted = new HashMap<String, ArrayList<RuleActionContainer>>();
    HashMap<String, String> variableAndValue = (HashMap<String, String>) container.getVariableAndValue();
    if (variableAndValue == null || variableAndValue.isEmpty()) {
        logger.warn("No rule target item with value found.");
        return toBeExecuted;
    }
    List<RuleSetBean> ruleSets = container.getImportDataTrueRuleSets();
    for (RuleSetBean ruleSet : ruleSets) {
        String key = getExpressionService().getItemOid(ruleSet.getOriginalTarget().getValue());
        List<RuleActionContainer> allActionContainerListBasedOnRuleExecutionResult = null;
        if (toBeExecuted.containsKey(key)) {
            allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
        } else {
            toBeExecuted.put(key, new ArrayList<RuleActionContainer>());
            allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
        }
        ItemDataBean itemData = null;
        for (ExpressionBean expressionBean : ruleSet.getExpressions()) {
            ruleSet.setTarget(expressionBean);
            for (RuleSetRuleBean ruleSetRule : ruleSet.getRuleSetRules()) {
                String result = null;
                RuleBean rule = ruleSetRule.getRuleBean();
                //ExpressionObjectWrapper eow = new ExpressionObjectWrapper(ds, currentStudy, rule.getExpression(), ruleSet, variableAndValue,ecb);
                ExpressionObjectWrapper eow = new ExpressionObjectWrapper(ds, study, rule.getExpression(), ruleSet, variableAndValue);
                try {
                    OpenClinicaExpressionParser oep = new OpenClinicaExpressionParser(eow);
                    result = (String) oep.parseAndEvaluateExpression(rule.getExpression().getValue());
                    itemData = getExpressionService().getItemDataBeanFromDb(ruleSet.getTarget().getValue());
                    // Actions
                    List<RuleActionBean> actionListBasedOnRuleExecutionResult = ruleSetRule.getActions(result, Phase.IMPORT);
                    if (itemData != null) {
                        Iterator<RuleActionBean> itr = actionListBasedOnRuleExecutionResult.iterator();
                        //String firstDDE = "firstDDEInsert_"+ruleSetRule.getOid()+"_"+itemData.getId();
                        while (itr.hasNext()) {
                            RuleActionBean ruleActionBean = itr.next();
                            /*
                                if(ruleActionBean.getActionType()==ActionType.INSERT) {
                                    request.setAttribute("insertAction", true);
                                    if(phase==Phase.DOUBLE_DATA_ENTRY && itemData.getStatus().getId()==4
                                            && request.getAttribute(firstDDE)==null) {
                                        request.setAttribute(firstDDE, true);
                                    }
                                }
                                if(request.getAttribute(firstDDE)==Boolean.TRUE) {
                                } else {
                                */
                            String itemDataValueFromImport = "";
                            if (variableAndValue.containsKey(key)) {
                                itemDataValueFromImport = variableAndValue.get(key);
                            } else {
                                logger.info("Cannot find value from variableAndValue for item=" + key + ". " + "Used itemData.getValue()");
                                itemDataValueFromImport = itemData.getValue();
                            }
                            RuleActionRunLogBean ruleActionRunLog = new RuleActionRunLogBean(ruleActionBean.getActionType(), itemData, itemDataValueFromImport, ruleSetRule.getRuleBean().getOid());
                            if (getRuleActionRunLogDao().findCountByRuleActionRunLogBean(ruleActionRunLog) > 0) {
                                itr.remove();
                            }
                        //}
                        }
                    }
                    for (RuleActionBean ruleActionBean : actionListBasedOnRuleExecutionResult) {
                        RuleActionContainer ruleActionContainer = new RuleActionContainer(ruleActionBean, expressionBean, itemData, ruleSet);
                        allActionContainerListBasedOnRuleExecutionResult.add(ruleActionContainer);
                    }
                    logger.info("RuleSet with target  : {} , Ran Rule : {}  The Result was : {} , Based on that {} action will be executed. ", new Object[] { ruleSet.getTarget().getValue(), rule.getName(), result, actionListBasedOnRuleExecutionResult.size() });
                } catch (OpenClinicaSystemException osa) {
                // TODO: report something useful
                }
            }
        }
    }
    return toBeExecuted;
}