static {
PATH_MAPPING.put("", "home_page");
PATH_MAPPING.put(PATH_LOGIN, "login");
PATH_MAPPING.put(PATH_LOGOUT, "login"); // !!! after logout we get redirected to /login
PATH_MAPPING.put(PATH_SIGNUP, "signup");
PATH_MAPPING.put(PATH_ERROR, "error");
PATH_MAPPING.put(PATH_FEED_ADMIN, "feed_admin");
PATH_MAPPING.put(PATH_SETTINGS, "settings");
PATH_MAPPING.put(PATH_FEEDS, "feeds");
PATH_MAPPING.put(PATH_FEED + "/*", "feed");
PATH_MAPPING.put(PATH_ADMIN, "admin");
}
public void init() throws ServletException {
super.init();
// allow = ThreddsConfig.getBoolean("NetcdfSubsetService.allow", true);
// String radarLevel2Dir = ThreddsConfig.get("NetcdfSubsetService.radarLevel2DataDir",
// "/data/ldm/pub/native/radar/level2/");
// if (!allow) return;
contentPath = ServletUtil.getContentPath();
rm = new RadarMethods(contentPath, logServerStartup);
// read in radarCollections.xml catalog
InvCatalogFactory factory = InvCatalogFactory.getDefaultFactory(false); // no validation
cat = readCatalog(factory, getPath() + catName, contentPath + getPath() + catName);
if (cat == null) {
logServerStartup.info("cat initialization failed");
return;
}
// URI tmpURI = cat.getBaseURI();
cat.setBaseURI(catURI);
// get path and location from cat
List parents = cat.getDatasets();
for (int i = 0; i < parents.size(); i++) {
InvDataset top = (InvDataset) parents.get(i);
datasets = top.getDatasets(); // dataset scans
for (int j = 0; j < datasets.size(); j++) {
InvDatasetScan ds = (InvDatasetScan) datasets.get(j);
if (ds.getPath() != null) {
dataLocation.put(ds.getPath(), ds.getScanLocation());
logServerStartup.info("path =" + ds.getPath() + " location =" + ds.getScanLocation());
}
ds.setXlinkHref(ds.getPath() + "/dataset.xml");
}
}
logServerStartup.info(getClass().getName() + " initialization complete ");
} // end init
/**
* Initializes the servlet context, based on the servlet context. Parses all context parameters
* and passes them on to the database context.
*
* @param sc servlet context
* @throws IOException I/O exception
*/
static synchronized void init(final ServletContext sc) throws IOException {
// skip process if context has already been initialized
if (context != null) return;
// set servlet path as home directory
final String path = sc.getRealPath("/");
System.setProperty(Prop.PATH, path);
// parse all context parameters
final HashMap<String, String> map = new HashMap<String, String>();
// store default web root
map.put(MainProp.HTTPPATH[0].toString(), path);
final Enumeration<?> en = sc.getInitParameterNames();
while (en.hasMoreElements()) {
final String key = en.nextElement().toString();
if (!key.startsWith(Prop.DBPREFIX)) continue;
// only consider parameters that start with "org.basex."
String val = sc.getInitParameter(key);
if (eq(key, DBUSER, DBPASS, DBMODE, DBVERBOSE)) {
// store servlet-specific parameters as system properties
System.setProperty(key, val);
} else {
// prefix relative paths with absolute servlet path
if (key.endsWith("path") && !new File(val).isAbsolute()) {
val = path + File.separator + val;
}
// store remaining parameters (without project prefix) in map
map.put(key.substring(Prop.DBPREFIX.length()).toUpperCase(Locale.ENGLISH), val);
}
}
context = new Context(map);
if (SERVER.equals(System.getProperty(DBMODE))) {
new BaseXServer(context);
} else {
context.log = new Log(context);
}
}
/** Returns a JarDiff for the given request */
public synchronized DownloadResponse getJarDiffEntry(
ResourceCatalog catalog, DownloadRequest dreq, JnlpResource res) {
if (dreq.getCurrentVersionId() == null) return null;
// check whether the request is from javaws 1.0/1.0.1
// do not generate minimal jardiff if it is from 1.0/1.0.1
boolean doJarDiffWorkAround = isJavawsVersion(dreq, "1.0*");
// First do a lookup to find a match
JarDiffKey key =
new JarDiffKey(
res.getName(),
dreq.getCurrentVersionId(),
res.getReturnVersionId(),
!doJarDiffWorkAround);
JarDiffEntry entry = (JarDiffEntry) _jarDiffEntries.get(key);
// If entry is not found, then the querty has not been made.
if (entry == null) {
if (_log.isInformationalLevel()) {
_log.addInformational(
"servlet.log.info.jardiff.gen",
res.getName(),
dreq.getCurrentVersionId(),
res.getReturnVersionId());
}
File f = generateJarDiff(catalog, dreq, res, doJarDiffWorkAround);
if (f == null) {
_log.addWarning(
"servlet.log.warning.jardiff.failed",
res.getName(),
dreq.getCurrentVersionId(),
res.getReturnVersionId());
}
// Store entry in table
entry = new JarDiffEntry(f);
_jarDiffEntries.put(key, entry);
}
// Check for no JarDiff to return
if (entry.getJarDiffFile() == null) {
return null;
} else {
return DownloadResponse.getFileDownloadResponse(
entry.getJarDiffFile(),
_jarDiffMimeType,
entry.getJarDiffFile().lastModified(),
res.getReturnVersionId());
}
}
public void init(FilterConfig filterConfig) {
this.config = filterConfig;
this.encoding = config.getInitParameter("encoding");
if (encoding == null || encoding.length() == 0) {
encoding = "GBK";
}
expiresMap = new HashMap();
Enumeration names = config.getInitParameterNames();
while (names.hasMoreElements()) {
String paramName = (String) names.nextElement();
if (!"encoding".equals(paramName)) {
String paramValue = config.getInitParameter(paramName);
try {
Integer expires = Integer.valueOf(config.getInitParameter(paramName));
expiresMap.put(paramName, expires);
} catch (Exception ex) {
// LogUtil.logError( "Filter."+paramValue+"="+paramValue);
}
}
}
}
public void init(ServletConfig config) throws ServletException {
super.init(config);
context = config.getServletContext();
TextProcessor tp = new CaseFolder();
try {
wikipedia =
new Wikipedia(
context.getInitParameter("mysql_server"),
context.getInitParameter("mysql_database"),
context.getInitParameter("mysql_user"),
context.getInitParameter("mysql_password"));
} catch (Exception e) {
throw new ServletException("Could not connect to wikipedia database.");
}
// Escaper escaper = new Escaper() ;
definer = new Definer(this);
comparer = new Comparer(this);
searcher = new Searcher(this);
try {
wikifier = new Wikifier(this, tp);
} catch (Exception e) {
System.err.println("Could not initialize wikifier");
}
try {
File dataDirectory = new File(context.getInitParameter("data_directory"));
if (!dataDirectory.exists() || !dataDirectory.isDirectory()) {
throw new Exception();
}
cachingThread = new CacherThread(dataDirectory, tp);
cachingThread.start();
} catch (Exception e) {
throw new ServletException("Could not locate wikipedia data directory.");
}
try {
TransformerFactory tf = TransformerFactory.newInstance();
transformersByName = new HashMap<String, Transformer>();
transformersByName.put(
"help", buildTransformer("help", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"loading", buildTransformer("loading", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"search", buildTransformer("search", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"compare", buildTransformer("compare", new File("/research/wikipediaminer/web/xsl"), tf));
transformersByName.put(
"wikify", buildTransformer("wikify", new File("/research/wikipediaminer/web/xsl"), tf));
Transformer serializer = TransformerFactory.newInstance().newTransformer();
serializer.setOutputProperty(OutputKeys.INDENT, "yes");
serializer.setOutputProperty(OutputKeys.METHOD, "xml");
serializer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
transformersByName.put("serializer", serializer);
} catch (Exception e) {
throw new ServletException("Could not load xslt library.");
}
}
public LoadItemVariantsBean() {
productVariants.put("ITM11_VARIANTS_1", "ITM16_PRODUCT_VARIANTS_1");
productVariants.put("ITM12_VARIANTS_2", "ITM17_PRODUCT_VARIANTS_2");
productVariants.put("ITM13_VARIANTS_3", "ITM18_PRODUCT_VARIANTS_3");
productVariants.put("ITM14_VARIANTS_4", "ITM19_PRODUCT_VARIANTS_4");
productVariants.put("ITM15_VARIANTS_5", "ITM20_PRODUCT_VARIANTS_5");
variantTypes.put("ITM11_VARIANTS_1", "ITM06_VARIANT_TYPES_1");
variantTypes.put("ITM12_VARIANTS_2", "ITM07_VARIANT_TYPES_2");
variantTypes.put("ITM13_VARIANTS_3", "ITM08_VARIANT_TYPES_3");
variantTypes.put("ITM14_VARIANTS_4", "ITM09_VARIANT_TYPES_4");
variantTypes.put("ITM15_VARIANTS_5", "ITM10_VARIANT_TYPES_5");
variantTypeJoins.put("ITM11_VARIANTS_1", "VARIANT_TYPE_ITM06");
variantTypeJoins.put("ITM12_VARIANTS_2", "VARIANT_TYPE_ITM07");
variantTypeJoins.put("ITM13_VARIANTS_3", "VARIANT_TYPE_ITM08");
variantTypeJoins.put("ITM14_VARIANTS_4", "VARIANT_TYPE_ITM09");
variantTypeJoins.put("ITM15_VARIANTS_5", "VARIANT_TYPE_ITM10");
variantCodeJoins.put("ITM11_VARIANTS_1", "VARIANT_CODE_ITM11");
variantCodeJoins.put("ITM12_VARIANTS_2", "VARIANT_CODE_ITM12");
variantCodeJoins.put("ITM13_VARIANTS_3", "VARIANT_CODE_ITM13");
variantCodeJoins.put("ITM14_VARIANTS_4", "VARIANT_CODE_ITM14");
variantCodeJoins.put("ITM15_VARIANTS_5", "VARIANT_CODE_ITM15");
}
/** Business logic to execute. */
public VOListResponse loadItemVariants(GridParams pars, String serverLanguageId, String username)
throws Throwable {
PreparedStatement pstmt = null;
Connection conn = null;
try {
if (this.conn == null) conn = getConn();
else conn = this.conn;
String tableName = (String) pars.getOtherGridParams().get(ApplicationConsts.TABLE_NAME);
ItemPK pk = (ItemPK) pars.getOtherGridParams().get(ApplicationConsts.ITEM_PK);
String productVariant = (String) productVariants.get(tableName);
String variantType = (String) variantTypes.get(tableName);
String variantTypeJoin = (String) variantTypeJoins.get(tableName);
String variantCodeJoin = (String) variantCodeJoins.get(tableName);
String sql =
"select "
+ tableName
+ "."
+ variantTypeJoin
+ ","
+ tableName
+ ".VARIANT_CODE,A.DESCRIPTION,B.DESCRIPTION, "
+ tableName
+ ".PROGRESSIVE_SYS10,"
+ variantType
+ ".PROGRESSIVE_SYS10 "
+ "from "
+ tableName
+ ","
+ variantType
+ ",SYS10_COMPANY_TRANSLATIONS A,SYS10_COMPANY_TRANSLATIONS B "
+ "where "
+ tableName
+ ".COMPANY_CODE_SYS01=? and "
+ tableName
+ ".COMPANY_CODE_SYS01="
+ variantType
+ ".COMPANY_CODE_SYS01 and "
+ tableName
+ "."
+ variantTypeJoin
+ "="
+ variantType
+ ".VARIANT_TYPE and "
+ tableName
+ ".COMPANY_CODE_SYS01=A.COMPANY_CODE_SYS01 and "
+ tableName
+ ".PROGRESSIVE_SYS10=A.PROGRESSIVE and A.LANGUAGE_CODE=? and "
+ variantType
+ ".COMPANY_CODE_SYS01=B.COMPANY_CODE_SYS01 and "
+ variantType
+ ".PROGRESSIVE_SYS10=B.PROGRESSIVE and B.LANGUAGE_CODE=? and "
+ tableName
+ ".ENABLED='Y' and "
+ variantType
+ ".ENABLED='Y' and "
+ // and not "+tableName+"."+variantTypeJoin+"=? and "+
"not "
+ tableName
+ ".VARIANT_CODE=? "
+ "order by "
+ tableName
+ "."
+ variantTypeJoin
+ ","
+ tableName
+ ".CODE_ORDER";
Map attribute2dbField = new HashMap();
attribute2dbField.put("variantType", tableName + "." + variantTypeJoin);
attribute2dbField.put("variantCode", tableName + ".VARIANT_CODE");
attribute2dbField.put("variantDesc", "A.DESCRIPTION");
attribute2dbField.put("variantTypeDesc", "B.DESCRIPTION");
attribute2dbField.put("variantProgressiveSys10", tableName + ".PROGRESSIVE_SYS10");
attribute2dbField.put("variantTypeProgressiveSys10", variantType + ".PROGRESSIVE_SYS10");
ArrayList values = new ArrayList();
values.add(pk.getCompanyCodeSys01ITM01());
values.add(serverLanguageId);
values.add(serverLanguageId);
// values.add(ApplicationConsts.JOLLY);
values.add(ApplicationConsts.JOLLY);
// read from ITMxxx table...
Response answer =
QueryUtil.getQuery(
conn,
new UserSessionParameters(username),
sql,
values,
attribute2dbField,
ItemVariantVO.class,
"Y",
"N",
null,
pars,
50,
true);
if (!answer.isError()) {
java.util.List vos = ((VOListResponse) answer).getRows();
HashMap map = new HashMap();
ItemVariantVO vo = null;
for (int i = 0; i < vos.size(); i++) {
vo = (ItemVariantVO) vos.get(i);
vo.setCompanyCodeSys01(pk.getCompanyCodeSys01ITM01());
vo.setItemCodeItm01(pk.getItemCodeITM01());
vo.setTableName(tableName);
map.put(vo.getVariantType() + "." + vo.getVariantCode(), vo);
}
pstmt =
conn.prepareStatement(
"select "
+ productVariant
+ "."
+ variantTypeJoin
+ ","
+ productVariant
+ "."
+ variantCodeJoin
+ " "
+ "from "
+ productVariant
+ " "
+ "where "
+ productVariant
+ ".COMPANY_CODE_SYS01=? and "
+ productVariant
+ ".ITEM_CODE_ITM01=? and "
+ productVariant
+ ".ENABLED='Y' ");
pstmt.setString(1, pk.getCompanyCodeSys01ITM01());
pstmt.setString(2, pk.getItemCodeITM01());
ResultSet rset = pstmt.executeQuery();
while (rset.next()) {
vo = (ItemVariantVO) map.get(rset.getString(1) + "." + rset.getString(2));
if (vo != null) vo.setSelected(Boolean.TRUE);
}
rset.close();
pstmt.close();
}
if (answer.isError()) throw new Exception(answer.getErrorMessage());
else return (VOListResponse) answer;
} catch (Throwable ex) {
Logger.error(
username,
this.getClass().getName(),
"getItemVariants",
"Error while fetching item variants list",
ex);
throw new Exception(ex.getMessage());
} finally {
try {
pstmt.close();
} catch (Exception ex2) {
}
try {
if (this.conn == null && conn != null) {
// close only local connection
conn.commit();
conn.close();
}
} catch (Exception exx) {
}
}
}
/** Business logic to execute. */
public final Response executeCommand(
Object inputPar,
UserSessionParameters userSessionPars,
HttpServletRequest request,
HttpServletResponse response,
HttpSession userSession,
ServletContext context) {
Connection conn = null;
PreparedStatement pstmt = null;
try {
conn = ConnectionManager.getConnection(context);
// fires the GenericEvent.CONNECTION_CREATED event...
EventsManager.getInstance()
.processEvent(
new GenericEvent(
this,
getRequestName(),
GenericEvent.CONNECTION_CREATED,
(JAIOUserSessionParameters) userSessionPars,
request,
response,
userSession,
context,
conn,
inputPar,
null));
Response responseVO =
bean.insertItem(
conn,
(JournalHeaderVO) inputPar,
userSessionPars,
request,
response,
userSession,
context);
if (responseVO.isError()) {
conn.rollback();
return responseVO;
}
if (inputPar instanceof JournalHeaderWithVatVO) {
JournalHeaderWithVatVO vo = (JournalHeaderWithVatVO) inputPar;
// insert vat rows in the specified vat register...
Response regRes =
vatRegisterAction.insertVatRows(
conn, vo.getVats(), userSessionPars, request, response, userSession, context);
if (regRes.isError()) {
conn.rollback();
return regRes;
}
// retrieve payment instalments...
Response payRes =
payAction.executeCommand(
new LookupValidationParams(vo.getPaymentCodeREG10(), new HashMap()),
userSessionPars,
request,
response,
userSession,
context);
if (payRes.isError()) {
conn.rollback();
return payRes;
}
PaymentVO payVO = (PaymentVO) ((VOListResponse) payRes).getRows().get(0);
GridParams gridParams = new GridParams();
gridParams
.getOtherGridParams()
.put(ApplicationConsts.PAYMENT_CODE_REG10, vo.getPaymentCodeREG10());
payRes =
paysAction.executeCommand(
gridParams, userSessionPars, request, response, userSession, context);
if (payRes.isError()) {
conn.rollback();
return payRes;
}
java.util.List rows = ((VOListResponse) payRes).getRows();
// create expirations in DOC19 ONLY if:
// - there are more than one instalment OR
// - there is only one instalment and this instalment has more than 0 instalment days
if (rows.size() > 1
|| (rows.size() == 1
&& ((PaymentInstalmentVO) rows.get(0)).getInstalmentDaysREG17().intValue() > 0)) {
// retrieve internationalization settings (Resources object)...
ServerResourcesFactory factory =
(ServerResourcesFactory) context.getAttribute(Controller.RESOURCES_FACTORY);
Resources resources = factory.getResources(userSessionPars.getLanguageId());
PaymentInstalmentVO inVO = null;
pstmt =
conn.prepareStatement(
"insert into DOC19_EXPIRATIONS(COMPANY_CODE_SYS01,DOC_TYPE,DOC_YEAR,DOC_NUMBER,DOC_SEQUENCE,PROGRESSIVE,DOC_DATE,EXPIRATION_DATE,NAME_1,NAME_2,VALUE,PAYED,DESCRIPTION,CUSTOMER_SUPPLIER_CODE,PROGRESSIVE_REG04,CURRENCY_CODE_REG03) values(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)");
long startTime = vo.getItemDateACC05().getTime(); // item date...
if (payVO.getStartDayREG10().equals(ApplicationConsts.START_DAY_END_MONTH)) {
Calendar cal = Calendar.getInstance();
if (cal.get(cal.MONTH) == 10
|| cal.get(cal.MONTH) == 3
|| cal.get(cal.MONTH) == 5
|| cal.get(cal.MONTH) == 8) cal.set(cal.DAY_OF_MONTH, 30);
else if (cal.get(cal.MONTH) == 1) {
if (cal.get(cal.YEAR) % 4 == 0) cal.set(cal.DAY_OF_MONTH, 29);
else cal.set(cal.DAY_OF_MONTH, 28);
} else cal.set(cal.DAY_OF_MONTH, 31);
startTime = cal.getTime().getTime();
}
BigDecimal amount = null;
for (int i = 0; i < rows.size(); i++) {
inVO = (PaymentInstalmentVO) rows.get(i);
pstmt.setString(1, vo.getCompanyCodeSys01ACC05());
pstmt.setString(2, vo.getDocTypeDOC19());
pstmt.setBigDecimal(3, vo.getItemYearACC05());
pstmt.setBigDecimal(4, null);
pstmt.setBigDecimal(5, vo.getDocSequenceDOC19());
pstmt.setBigDecimal(
6,
ProgressiveUtils.getConsecutiveProgressive(
"DOC19_EXPIRATIONS", "PROGRESSIVE", conn));
pstmt.setDate(7, vo.getItemDateACC05());
pstmt.setDate(
8,
new java.sql.Date(
startTime
+ inVO.getInstalmentDaysREG17().longValue()
* 86400
* 1000)); // expiration date
pstmt.setString(9, vo.getName_1REG04());
pstmt.setString(10, vo.getName_2REG04());
amount =
vo.getTotalValue()
.multiply(inVO.getPercentageREG17())
.divide(new BigDecimal(100), BigDecimal.ROUND_HALF_UP)
.setScale(vo.getTotalValue().scale(), BigDecimal.ROUND_HALF_UP); // value
pstmt.setBigDecimal(11, amount);
pstmt.setString(12, "N");
if (vo.getDocTypeDOC19().equals(ApplicationConsts.SALE_GENERIC_INVOICE))
pstmt.setString(
13,
resources.getResource("sale generic document")
+ " "
+ vo.getDocSequenceDOC19()
+ "/"
+ vo.getItemYearACC05()
+ " - "
+ resources.getResource("valueREG01")
+ " "
+ resources.getResource("rateNumberREG17")
+ " "
+ (i + 1)
+ " - "
+ inVO.getPaymentTypeDescriptionSYS10()); // description
else
pstmt.setString(
13,
resources.getResource("purchase generic document")
+ " "
+ vo.getDocSequenceDOC19()
+ "/"
+ vo.getItemYearACC05()
+ " - "
+ resources.getResource("valueREG01")
+ " "
+ resources.getResource("rateNumberREG17")
+ " "
+ (i + 1)
+ " - "
+ inVO.getPaymentTypeDescriptionSYS10()); // description
pstmt.setString(14, vo.getCustomerCodeSAL07());
pstmt.setBigDecimal(15, vo.getProgressiveREG04());
pstmt.setString(16, vo.getCurrencyCodeREG01());
pstmt.execute();
}
pstmt.close();
}
// create an item registration for proceeds, according to expiration settings (e.g. retail
// selling):
// there must be only one instalment and this instalment has 0 instalment days
if (rows.size() == 1
&& ((PaymentInstalmentVO) rows.get(0)).getInstalmentDaysREG17().intValue() == 0) {
// retrieve internationalization settings (Resources object)...
ServerResourcesFactory factory =
(ServerResourcesFactory) context.getAttribute(Controller.RESOURCES_FACTORY);
Resources resources = factory.getResources(userSessionPars.getLanguageId());
HashMap map = new HashMap();
map.put(ApplicationConsts.COMPANY_CODE_SYS01, vo.getCompanyCodeSys01ACC05());
map.put(ApplicationConsts.PARAM_CODE, ApplicationConsts.CASE_ACCOUNT);
Response res =
userParamAction.executeCommand(
map, userSessionPars, request, response, userSession, context);
if (res.isError()) {
conn.rollback();
return res;
}
String caseAccountCode = ((VOResponse) res).getVo().toString();
JournalHeaderVO jhVO = new JournalHeaderVO();
jhVO.setCompanyCodeSys01ACC05(vo.getCompanyCodeSys01ACC05());
if (vo.getDocTypeDOC19().equals(ApplicationConsts.SALE_GENERIC_INVOICE)) {
jhVO.setDescriptionACC05(
resources.getResource("sale generic document")
+ " "
+ vo.getDocSequenceDOC19()
+ "/"
+ vo.getItemYearACC05()
+ " - "
+ resources.getResource("customer")
+ " "
+ vo.getName_1REG04()
+ " "
+ (vo.getName_2REG04() == null ? "" : vo.getName_2REG04()));
jhVO.setAccountingMotiveCodeAcc03ACC05(ApplicationConsts.MOTIVE_INVOICE_PROCEEDS);
} else {
jhVO.setDescriptionACC05(
resources.getResource("purchase generic document")
+ " "
+ vo.getDocSequenceDOC19()
+ "/"
+ vo.getItemYearACC05()
+ " - "
+ resources.getResource("supplier")
+ " "
+ vo.getName_1REG04()
+ " "
+ (vo.getName_2REG04() == null ? "" : vo.getName_2REG04()));
jhVO.setAccountingMotiveCodeAcc03ACC05(ApplicationConsts.MOTIVE_PURCHASE_INVOICE_PAYED);
}
jhVO.setItemDateACC05(new java.sql.Date(System.currentTimeMillis()));
jhVO.setItemYearACC05(new BigDecimal(Calendar.getInstance().get(Calendar.YEAR)));
JournalRowVO jrVO = new JournalRowVO();
jrVO.setCompanyCodeSys01ACC06(jhVO.getCompanyCodeSys01ACC05());
if (vo.getDocTypeDOC19().equals(ApplicationConsts.SALE_GENERIC_INVOICE)) {
jrVO.setAccountCodeAcc02ACC06(vo.getCreditAccountCodeAcc02SAL07());
jrVO.setAccountCodeACC06(vo.getCustomerCodeSAL07());
jrVO.setAccountCodeTypeACC06(ApplicationConsts.ACCOUNT_TYPE_CUSTOMER);
jrVO.setCreditAmountACC06(vo.getTotalValue());
} else {
jrVO.setAccountCodeAcc02ACC06(vo.getDebitAccountCodeAcc02PUR01());
jrVO.setAccountCodeACC06(vo.getSupplierCodePUR01());
jrVO.setAccountCodeTypeACC06(ApplicationConsts.ACCOUNT_TYPE_SUPPLIER);
jrVO.setDebitAmountACC06(vo.getTotalValue());
}
jrVO.setDescriptionACC06("");
jrVO.setItemYearAcc05ACC06(jhVO.getItemYearACC05());
jrVO.setProgressiveAcc05ACC06(jhVO.getProgressiveACC05());
jhVO.addJournalRow(jrVO);
jrVO = new JournalRowVO();
jrVO.setCompanyCodeSys01ACC06(jhVO.getCompanyCodeSys01ACC05());
jrVO.setAccountCodeAcc02ACC06(caseAccountCode);
jrVO.setAccountCodeACC06(caseAccountCode);
jrVO.setAccountCodeTypeACC06(ApplicationConsts.ACCOUNT_TYPE_ACCOUNT);
if (vo.getDocTypeDOC19().equals(ApplicationConsts.SALE_GENERIC_INVOICE)) {
jrVO.setDebitAmountACC06(vo.getTotalValue());
} else {
jrVO.setCreditAmountACC06(vo.getTotalValue());
}
jrVO.setDescriptionACC06("");
jrVO.setItemYearAcc05ACC06(jhVO.getItemYearACC05());
jrVO.setProgressiveAcc05ACC06(jhVO.getProgressiveACC05());
jhVO.addJournalRow(jrVO);
Response proceedsRes =
bean.insertItem(conn, jhVO, userSessionPars, request, response, userSession, context);
if (proceedsRes.isError()) {
conn.rollback();
return proceedsRes;
}
}
}
Response answer = responseVO;
// fires the GenericEvent.BEFORE_COMMIT event...
EventsManager.getInstance()
.processEvent(
new GenericEvent(
this,
getRequestName(),
GenericEvent.BEFORE_COMMIT,
(JAIOUserSessionParameters) userSessionPars,
request,
response,
userSession,
context,
conn,
inputPar,
answer));
conn.commit();
// fires the GenericEvent.AFTER_COMMIT event...
EventsManager.getInstance()
.processEvent(
new GenericEvent(
this,
getRequestName(),
GenericEvent.AFTER_COMMIT,
(JAIOUserSessionParameters) userSessionPars,
request,
response,
userSession,
context,
conn,
inputPar,
answer));
return answer;
} catch (Throwable ex) {
Logger.error(
userSessionPars.getUsername(),
this.getClass().getName(),
"executeCommand",
"Error while inserting a new item in the journal",
ex);
try {
conn.rollback();
} catch (Exception ex3) {
}
return new ErrorResponse(ex.getMessage());
} finally {
try {
pstmt.close();
} catch (Exception ex2) {
}
try {
ConnectionManager.releaseConnection(conn, context);
} catch (Exception ex1) {
}
}
}
/**
* Processes requests for both HTTP <code>GET</code> and <code>POST</code> methods.
*
* @param request servlet request
* @param response servlet response
* @throws javax.servlet.ServletException if a servlet-specific error occurs
* @throws java.io.IOException if an I/O error occurs
*/
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws IOException, ServletException {
XDebug xdebug = new XDebug();
xdebug.startTimer();
response.setContentType("application/json");
PrintWriter writer = response.getWriter();
try {
List resultsList = new LinkedList();
// Get the gene list
String geneList = request.getParameter(QueryBuilder.GENE_LIST);
if (request instanceof XssRequestWrapper) {
geneList = ((XssRequestWrapper) request).getRawParameter(QueryBuilder.GENE_LIST);
}
String cancerStudyIdListString = request.getParameter(QueryBuilder.CANCER_STUDY_LIST);
String[] cancerStudyIdList = cancerStudyIdListString.split(",");
// Get the priority
Integer dataTypePriority;
try {
dataTypePriority =
Integer.parseInt(request.getParameter(QueryBuilder.DATA_PRIORITY).trim());
} catch (NumberFormatException e) {
dataTypePriority = 0;
}
// Cancer All Cancer Studies
List<CancerStudy> cancerStudiesList = accessControl.getCancerStudies();
HashMap<String, Boolean> studyMap = new HashMap<>();
for (String studyId : cancerStudyIdList) {
studyMap.put(studyId, Boolean.TRUE);
}
for (CancerStudy cancerStudy : cancerStudiesList) {
String cancerStudyId = cancerStudy.getCancerStudyStableId();
if (!studyMap.containsKey(cancerStudyId)) {
continue;
}
if (cancerStudyId.equalsIgnoreCase("all")) continue;
Map cancerMap = new LinkedHashMap();
cancerMap.put("studyId", cancerStudyId);
cancerMap.put("typeOfCancer", cancerStudy.getTypeOfCancerId());
// Get all Genetic Profiles Associated with this Cancer Study ID.
ArrayList<GeneticProfile> geneticProfileList =
GetGeneticProfiles.getGeneticProfiles(cancerStudyId);
// Get all Patient Lists Associated with this Cancer Study ID.
ArrayList<SampleList> sampleSetList = GetSampleLists.getSampleLists(cancerStudyId);
// Get the default patient set
AnnotatedSampleSets annotatedSampleSets =
new AnnotatedSampleSets(sampleSetList, dataTypePriority);
SampleList defaultSampleSet = annotatedSampleSets.getDefaultSampleList();
if (defaultSampleSet == null) {
continue;
}
List<String> sampleIds = defaultSampleSet.getSampleList();
// Get the default genomic profiles
CategorizedGeneticProfileSet categorizedGeneticProfileSet =
new CategorizedGeneticProfileSet(geneticProfileList);
HashMap<String, GeneticProfile> defaultGeneticProfileSet = null;
switch (dataTypePriority) {
case 2:
defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultCopyNumberMap();
break;
case 1:
defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultMutationMap();
break;
case 0:
default:
defaultGeneticProfileSet =
categorizedGeneticProfileSet.getDefaultMutationAndCopyNumberMap();
}
String mutationProfile = "", cnaProfile = "";
for (GeneticProfile geneticProfile : defaultGeneticProfileSet.values()) {
GeneticAlterationType geneticAlterationType = geneticProfile.getGeneticAlterationType();
if (geneticAlterationType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION)) {
cnaProfile = geneticProfile.getStableId();
} else if (geneticAlterationType.equals(GeneticAlterationType.MUTATION_EXTENDED)) {
mutationProfile = geneticProfile.getStableId();
}
}
cancerMap.put("mutationProfile", mutationProfile);
cancerMap.put("cnaProfile", cnaProfile);
cancerMap.put("caseSetId", defaultSampleSet.getStableId());
cancerMap.put("caseSetLength", sampleIds.size());
ProfileDataSummary genomicData =
getGenomicData(
cancerStudyId,
defaultGeneticProfileSet,
defaultSampleSet,
geneList,
sampleSetList,
request,
response);
ArrayList<GeneWithScore> geneFrequencyList = genomicData.getGeneFrequencyList();
ArrayList<String> genes = new ArrayList<String>();
for (GeneWithScore geneWithScore : geneFrequencyList) genes.add(geneWithScore.getGene());
int noOfMutated = 0,
noOfCnaUp = 0,
noOfCnaDown = 0,
noOfCnaLoss = 0,
noOfCnaGain = 0,
noOfOther = 0,
noOfAll = 0;
boolean skipStudy = defaultGeneticProfileSet.isEmpty();
if (!skipStudy) {
for (String sampleId : sampleIds) {
if (sampleId == null) {
continue;
}
if (!genomicData.isCaseAltered(sampleId)) continue;
boolean isAnyMutated = false,
isAnyCnaUp = false,
isAnyCnaDown = false,
isAnyCnaLoss = false,
isAnyCnaGain = false;
for (String gene : genes) {
isAnyMutated |= genomicData.isGeneMutated(gene, sampleId);
GeneticTypeLevel cnaLevel = genomicData.getCNALevel(gene, sampleId);
boolean isCnaUp = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Amplified);
isAnyCnaUp |= isCnaUp;
boolean isCnaDown =
cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HomozygouslyDeleted);
isAnyCnaDown |= isCnaDown;
boolean isCnaLoss =
cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HemizygouslyDeleted);
isAnyCnaLoss |= isCnaLoss;
boolean isCnaGain = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Gained);
isAnyCnaGain |= isCnaGain;
}
boolean isAnyCnaChanged = isAnyCnaUp || isAnyCnaDown;
if (isAnyMutated && !isAnyCnaChanged) noOfMutated++;
else if (isAnyMutated && isAnyCnaChanged) noOfOther++;
else if (isAnyCnaUp) noOfCnaUp++;
else if (isAnyCnaDown) noOfCnaDown++;
else if (isAnyCnaGain) noOfCnaGain++;
else if (isAnyCnaLoss) noOfCnaLoss++;
noOfAll++;
}
}
Map alterations = new LinkedHashMap();
cancerMap.put("alterations", alterations);
alterations.put("all", noOfAll);
alterations.put("mutation", noOfMutated);
alterations.put("cnaUp", noOfCnaUp);
alterations.put("cnaDown", noOfCnaDown);
alterations.put("cnaLoss", noOfCnaLoss);
alterations.put("cnaGain", noOfCnaGain);
alterations.put("other", noOfOther);
cancerMap.put("genes", genes);
cancerMap.put("skipped", skipStudy);
resultsList.add(cancerMap);
}
JSONValue.writeJSONString(resultsList, writer);
} catch (DaoException e) {
throw new ServletException(e);
} catch (ProtocolException e) {
throw new ServletException(e);
} finally {
writer.close();
}
}
private static Interpreter getInterpreter(String contextId) throws EvalError {
// Get the appropriate interpreter
Interpreter i = null;
boolean createdInterp = false;
synchronized (interpreters) { // serialize two gets of the same name
i = interpreters.get(contextId);
if (i == null) {
i = new Interpreter();
interpreters.put(contextId, i);
createdInterp = true;
}
}
if (createdInterp) {
Log.log("Created context: " + contextId + " (" + i + ")");
// Now configure stdin and stdout to capture 10k of content
// Store references to the circular buffers within the interpreter itself.
// This provides a nice place to store them plus theoretically allows
// advanced use from within the bsh environment.
// On Windows print() outputs \r\n but in XQuery that's normalized to \n
// so the 10k of Java buffer may produce less than 10k of content in XQuery!
OutputStream circularOutput = new CircularByteArrayOutputStream(10240);
PrintStream printOutput = new PrintStream(circularOutput);
i.setOut(printOutput);
i.set("mljamout", circularOutput);
OutputStream circularError = new CircularByteArrayOutputStream(10240);
PrintStream printError = new PrintStream(circularError);
i.setErr(printError);
i.set("mljamerr", circularError);
// Capture the built-in System.out and System.err also.
// (Commented out since System appears global, can't do per interpreter.)
// i.set("mljamprintout", printOutput);
// i.set("mljamprinterr", printError);
// i.eval("System.setOut(mljamprintout);");
// i.eval("System.setErr(mljamprinterr);");
// Need to expose hexdecode() and base64decode() built-in functions
i.eval("hexdecode(String s) { return com.xqdev.jam.MLJAM.hexDecode(s); }");
i.eval("base64decode(String s) { return com.xqdev.jam.MLJAM.base64Decode(s); }");
// Let's tell the context what its id is
i.set("mljamid", contextId);
}
// Update the last accessed time, used for cleaning
i.set("mljamlast", System.currentTimeMillis());
// If it's been long enough, go snooping for stale contexts
if (System.currentTimeMillis() > lastClean + CLEAN_INTERVAL) {
Log.log("Initiated periodic scan for stale context objects");
lastClean = System.currentTimeMillis();
Iterator<Interpreter> itr = interpreters.values().iterator();
while (itr.hasNext()) {
Interpreter interp = itr.next();
Long last = (Long) interp.get("mljamlast");
if (System.currentTimeMillis() > last + STALE_TIMEOUT) {
itr.remove();
Log.log("Staled context: " + interp.get("mljamid") + " (" + interp + ")");
} else if ((System.currentTimeMillis() > last + TEMP_STALE_TIMEOUT)
&& ("" + interp.get("mljamid")).startsWith("temp:")) {
itr.remove();
Log.log("Staled temp context: " + interp.get("mljamid") + " (" + interp + ")");
}
}
}
return i;
}