public void setResourceLoader(ResourceLoader resourceLoader) {
this.resourceLoader = resourceLoader;
try {
// setPROPERTIES_DIR();
webapp = getWebAppName(resourceLoader.getResource("/").getURI().getPath());
logMe("is web app name null?" + webapp);
String dbName = dataInfo.getProperty("dbType");
DATAINFO = dataInfo;
dataInfo =
setDataInfoProperties(); // weird, but there are references to dataInfo...MainMenuServlet
// for instance
// setDataInfoPath();
EXTRACTINFO = extractInfo;
DB_NAME = dbName;
SQLFactory factory = SQLFactory.getInstance();
factory.run(dbName, resourceLoader);
copyBaseToDest(resourceLoader);
extractProperties = findExtractProperties();
// tbh, following line to be removed
// reportUrl();
} catch (OpenClinicaSystemException e) {
logger.debug(e.getMessage());
logger.debug(e.toString());
throw new OpenClinicaSystemException(e.getMessage(), e.fillInStackTrace());
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void copyBaseToDest(ResourceLoader resourceLoader) {
// System.out.println("Properties directory?"+resourceLoader.getResource("properties/xslt"));
ByteArrayInputStream listSrcFiles[] = new ByteArrayInputStream[10];
String[] fileNames = {
"odm_spss_dat.xsl",
"ODMToTAB.xsl",
"odm_to_html.xsl",
"odm_to_xslfo.xsl",
"ODM-XSLFO-Stylesheet.xsl",
"odm_spss_sps.xsl",
"copyXML.xsl",
"odm1.3_to_1.2.xsl",
"odm1.3_to_1.2_extensions.xsl"
};
try {
listSrcFiles[0] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[0])
.getInputStream();
listSrcFiles[1] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[1])
.getInputStream();
listSrcFiles[2] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[2])
.getInputStream();
listSrcFiles[3] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[3])
.getInputStream();
listSrcFiles[4] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[4])
.getInputStream();
listSrcFiles[5] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[5])
.getInputStream();
listSrcFiles[6] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[6])
.getInputStream();
listSrcFiles[7] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[7])
.getInputStream();
listSrcFiles[8] =
(ByteArrayInputStream)
resourceLoader
.getResource(
"classpath:properties"
+ File.separator
+ "xslt"
+ File.separator
+ fileNames[8])
.getInputStream();
} catch (IOException ioe) {
OpenClinicaSystemException oe = new OpenClinicaSystemException("Unable to read source files");
oe.initCause(ioe);
oe.setStackTrace(ioe.getStackTrace());
logger.debug(ioe.getMessage());
throw oe;
}
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 (int i = 0; i < fileNames.length; i++) {
File dest1 = new File(dest, fileNames[i]);
// File src1 = listSrcFiles[i];
if (listSrcFiles[i] != null) copyFiles(listSrcFiles[i], dest1);
}
}
private void copyFiles(ByteArrayInputStream fis, File dest) {
FileOutputStream fos = null;
byte[] buffer = new byte[512]; // Buffer 4K at a time (you can change this).
int bytesRead;
logger.debug("fis?" + fis);
try {
fos = new FileOutputStream(dest);
while ((bytesRead = fis.read(buffer)) >= 0) {
fos.write(buffer, 0, bytesRead);
}
} catch (IOException ioe) { // error while copying files
OpenClinicaSystemException oe =
new OpenClinicaSystemException(
"Unable to copy file: "
+ fis
+ "to"
+ dest.getAbsolutePath()
+ "."
+ dest.getAbsolutePath()
+ ".");
oe.initCause(ioe);
oe.setStackTrace(ioe.getStackTrace());
throw oe;
} finally { // Ensure that the files are closed (if they were open).
if (fis != null) {
try {
fis.close();
} catch (IOException ioe) {
OpenClinicaSystemException oe =
new OpenClinicaSystemException(
"Unable to copy file: "
+ fis
+ "to"
+ dest.getAbsolutePath()
+ "."
+ dest.getAbsolutePath()
+ ".");
oe.initCause(ioe);
oe.setStackTrace(ioe.getStackTrace());
logger.debug(ioe.getMessage());
throw oe;
}
}
if (fos != null) {
try {
fos.close();
} catch (IOException ioe) {
OpenClinicaSystemException oe =
new OpenClinicaSystemException(
"Unable to copy file: "
+ fis
+ "to"
+ dest.getAbsolutePath()
+ "."
+ dest.getAbsolutePath()
+ ".");
oe.initCause(ioe);
oe.setStackTrace(ioe.getStackTrace());
logger.debug(ioe.getMessage());
throw oe;
}
}
}
}
public HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>>
runRulesBulk(
List<RuleSetBean> ruleSets,
Boolean dryRun,
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>>>();
for (RuleSetBean ruleSet : ruleSets) {
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 = oep.parseAndEvaluateExpression(rule.getExpression().getValue());
// Actions
List<RuleActionBean> actionListBasedOnRuleExecutionResult =
ruleSetRule.getActions(result);
if (dryRun && actionListBasedOnRuleExecutionResult.size() > 0) {
crfViewSpecificOrderedObjects =
populateForCrfBasedRulesView(
crfViewSpecificOrderedObjects,
ruleSet,
rule,
result,
currentStudy,
actionListBasedOnRuleExecutionResult);
}
// If not a dryRun meaning run Actions
if (!dryRun) {
for (RuleActionBean ruleAction : actionListBasedOnRuleExecutionResult) {
int itemDataBeanId =
getExpressionService()
.getItemDataBeanFromDb(ruleSet.getTarget().getValue())
.getId();
ruleAction.setCuratedMessage(curateMessage(ruleAction, ruleSetRule));
// getDiscrepancyNoteService().saveFieldNotes(ruleAction.getSummary(),
// itemDataBeanId, "ItemData", currentStudy, ub);
ActionProcessor ap =
ActionProcessorFacade.getActionProcessor(ruleAction.getActionType(), ds);
ap.execute(
ruleAction,
itemDataBeanId,
"ItemData",
currentStudy,
ub,
prepareEmailContents(ruleSet, ruleSetRule, currentStudy, ruleAction));
}
}
} catch (OpenClinicaSystemException osa) {
// TODO: Auditing might happen here failed rule
logger.warn(
"RuleSet with target : {} , Ran Rule : {} , It resulted in an error due to : {}",
new Object[] {ruleSet.getTarget().getValue(), rule.getName(), osa.getMessage()});
}
}
}
}
logCrfViewSpecificOrderedObjects(crfViewSpecificOrderedObjects);
return crfViewSpecificOrderedObjects;
}