public ReaderHandler(LowLevelDbAccess lowLevelDbAccess, String webDir) {
loginInfoDb = new LoginInfo.DB(lowLevelDbAccess);
userDb = new User.DB(lowLevelDbAccess);
feedDb = new Feed.DB(lowLevelDbAccess);
articleDb = new Article.DB(lowLevelDbAccess);
readArticlesCollDb = new ReadArticlesColl.DB(lowLevelDbAccess);
userHelpers = new UserHelpers(loginInfoDb, userDb);
setContextPath("/");
File warPath = new File(webDir);
setWar(warPath.getAbsolutePath());
if (isInJar) {
for (Map.Entry<String, String> entry : PATH_MAPPING.entrySet()) {
addPrebuiltJsp(entry.getKey(), "jsp." + entry.getValue().replaceAll("_", "_005f") + "_jsp");
}
} else {
for (Map.Entry<String, String> entry : PATH_MAPPING.entrySet()) {
addServlet(
new ServletHolder(new RedirectServlet("/" + entry.getValue() + ".jsp")),
entry.getKey());
}
}
setErrorHandler(new ReaderErrorHandler());
}
private static void endInterpreter(String contextId) throws EvalError {
Interpreter i = interpreters.get(contextId);
if (i == null) return;
i.eval("clear();"); // can't hurt to tell bsh to clean up internally
interpreters.remove(contextId); // now wait for GC
Log.log("Destroyed context: " + contextId + " (" + i + ")");
}
/** Gets all Genomic Data. */
private ProfileDataSummary getGenomicData(
String cancerStudyId,
HashMap<String, GeneticProfile> defaultGeneticProfileSet,
SampleList defaultSampleSet,
String geneListStr,
ArrayList<SampleList> sampleList,
HttpServletRequest request,
HttpServletResponse response)
throws IOException, ServletException, DaoException {
// parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
double zScore =
ZScoreUtil.getZScore(
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
request);
double rppaScore = ZScoreUtil.getRPPAScore(request);
ParserOutput theOncoPrintSpecParserOutput =
OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(
geneListStr,
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
zScore,
rppaScore);
ArrayList<String> geneList = new ArrayList<String>();
geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes());
ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
Set<String> warningUnion = new HashSet<String>();
for (GeneticProfile profile : defaultGeneticProfileSet.values()) {
try {
GetProfileData remoteCall =
new GetProfileData(
profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " "));
ProfileData pData = remoteCall.getProfileData();
warningUnion.addAll(remoteCall.getWarnings());
profileDataList.add(pData);
} catch (IllegalArgumentException e) {
e.getStackTrace();
}
}
ProfileMerger merger = new ProfileMerger(profileDataList);
ProfileData mergedProfile = merger.getMergedProfile();
ProfileDataSummary dataSummary =
new ProfileDataSummary(
mergedProfile,
theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(),
zScore,
rppaScore);
return dataSummary;
}
/**
* Returns true if the user represented by the current request plays the named role.
*
* @param role the named role to test.
* @return true if the user plays the role.
*/
public boolean isUserInRole(String role) {
ServletInvocation invocation = getInvocation();
if (invocation == null) {
if (getRequest() != null) return getRequest().isUserInRole(role);
else return false;
}
HashMap<String, String> roleMap = invocation.getSecurityRoleMap();
if (roleMap != null) {
String linkRole = roleMap.get(role);
if (linkRole != null) role = linkRole;
}
String runAs = getRunAs();
if (runAs != null) return runAs.equals(role);
WebApp webApp = getWebApp();
Principal user = getUserPrincipal();
if (user == null) {
if (log.isLoggable(Level.FINE)) log.fine(this + " no user for isUserInRole");
return false;
}
RoleMapManager roleManager = webApp != null ? webApp.getRoleMapManager() : null;
if (roleManager != null) {
Boolean result = roleManager.isUserInRole(role, user);
if (result != null) {
if (log.isLoggable(Level.FINE)) log.fine(this + " userInRole(" + role + ")->" + result);
return result;
}
}
Login login = webApp == null ? null : webApp.getLogin();
boolean inRole = login != null && login.isUserInRole(user, role);
if (log.isLoggable(Level.FINE)) {
if (login == null) log.fine(this + " no Login for isUserInRole");
else if (user == null) log.fine(this + " no user for isUserInRole");
else if (inRole) log.fine(this + " " + user + " is in role: " + role);
else log.fine(this + " failed " + user + " in role: " + role);
}
return inRole;
}
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");
}
/** 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());
}
}
private String getShortcutScript(HashMap<String, String> usedButtonShortCuts) {
StringBuffer shortcuts = new StringBuffer();
shortcuts.append(" function buttonListShorcuts() {\n");
Iterator<String> ik = usedButtonShortCuts.keySet().iterator();
Iterator<String> iv = usedButtonShortCuts.values().iterator();
while (ik.hasNext() && iv.hasNext()) {
shortcuts
.append(" keyArray[keyArray.length] = new keyArrayItem(\"")
.append(ik.next())
.append("\", \"")
.append(iv.next())
.append("\", null, \"altKey\", false, \"onkeydown\");\n");
}
shortcuts.append(" return true;\n}");
return shortcuts.toString();
}
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
/**
* 把数据源HashMap转换成json
*
* @param map
*/
public static String hashMapToJson(HashMap map) {
String string = "{";
for (Iterator it = map.entrySet().iterator(); it.hasNext(); ) {
Entry e = (Entry) it.next();
string += "'" + e.getKey() + "':";
string += "'" + e.getValue() + "',";
}
string = string.substring(0, string.lastIndexOf(","));
string += "}";
return string;
}
private String getServerAddress(String servletName) {
// System.out.println("finding server for "+servletName);
Integer res = methodHashCodesToClusterIds.get(servletName.hashCode());
if (res != null) {
// System.out.println("servlet "+servletName+" going to "+res);
return serverAddresses[res % numberOfServers];
} else {
// System.out.println("could not find info on servlet "+servletName);
return serverAddresses[0];
}
}
/**
* 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);
}
}
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);
}
}
}
}
private void setResponseHeader(
HttpServletResponse response, String uri, String transferEncoding) {
// LogUtil.logDebug( uri + ".Accept-Encoding: "+ transferEncoding);
String ext = null;
int dot = uri.lastIndexOf(".");
if (dot != -1) {
ext = uri.substring(dot + 1);
}
if (ext != null && ext.length() > 0) {
Integer expires = (Integer) expiresMap.get(ext);
if (expires != null) {
// LogUtil.logDebug( uri + ".Expires: "+ expires.intValue());
if (expires.intValue() > 0) {
response.setHeader("Cache-Control", "max-age=" + expires.intValue()); // HTTP 1.1
} else {
response.setHeader("Cache-Control", "no-cache");
response.setHeader("Pragma", "no-cache"); // HTTP 1.0
response.setDateHeader("Expires", expires.intValue());
}
}
}
}
public LDAPolicy(String[] serverAddresses) {
super(serverAddresses);
numberOfServers = serverAddresses.length;
serverRequests = new int[numberOfServers];
// System.out.println("Loading input data from "+localPath);
servletNameToClusterIds =
(HashMap<String, Integer>)
DataReader.loadSerializedObject(localPath + "servletNameToClusterId.serialized");
methodHashCodesToClusterIds =
(HashMap<Integer, Integer>)
DataReader.loadSerializedObject(localPath + "hashCodesToClusterIds.serialized");
if (servletNameToClusterIds != null && methodHashCodesToClusterIds != null) {
for (String s : servletNameToClusterIds.keySet()) {
// System.out.println("Servlet["+s+"] in
// cluster["+methodHashCodesToClusterIds.get(s.hashCode())+"]");
}
} else {
throw new Error(
"Could not load properly the load balancing input data. Terminating application");
}
}
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) {
}
}
}
private void datasetInfoXml(RadarType radarType, String pathInfo, PrintWriter pw)
throws IOException {
try {
pw.println(
"<catalog xmlns=\"http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" name=\"Radar Data\" version=\"1.0.1\">\n");
// add service
pw.println(
" <service name=\"radarServer\" base=\"/thredds/radarServer/\" serviceType=\"DQC\" />\n");
pathInfo = pathInfo.replace("/dataset.xml", "");
pathInfo = pathInfo.replace("/catalog.xml", "");
if (pathInfo.startsWith("/")) pathInfo = pathInfo.substring(1);
for (int i = 0; i < datasets.size(); i++) {
InvDatasetScan ds = (InvDatasetScan) datasets.get(i);
if (!(pathInfo.equals(ds.getPath()))) {
continue;
}
pw.println(" <dataset ID=\"" + ds.getID() + "\" serviceName=\"radarServer\">");
pw.println(" <urlpath>" + ds.getPath() + "</urlpath>");
pw.println(" <dataType>" + ds.getDataType() + "</dataType>");
pw.println(" <dataFormat>" + ds.getDataFormatType() + "</dataFormat>");
pw.println(" <serviceName>radarServer</serviceName>");
pw.println(" <metadata inherited=\"true\">");
pw.println(" <documentation type=\"summary\">" + ds.getSummary() + "</documentation>");
CalendarDateRange dr = ds.getCalendarDateCoverage();
pw.println(" <TimeSpan>");
pw.print(" <start>");
if (pathInfo.contains("IDD")) {
pw.print(rm.getStartDateTime(ds.getPath()));
} else {
pw.print(dr.getStart().toString());
}
pw.println("</start>");
pw.println(" <end>" + dr.getEnd().toString() + "</end>");
pw.println(" </TimeSpan>");
ThreddsMetadata.GeospatialCoverage gc = ds.getGeospatialCoverage();
LatLonRect bb = new LatLonRect();
gc.setBoundingBox(bb);
pw.println(" <LatLonBox>");
pw.println(" <north>" + gc.getLatNorth() + "</north>");
pw.println(" <south>" + gc.getLatSouth() + "</south>");
pw.println(" <east>" + gc.getLonEast() + "</east>");
pw.println(" <west>" + gc.getLonWest() + "</west>");
pw.println(" </LatLonBox>");
ThreddsMetadata.Variables cvs = (ThreddsMetadata.Variables) ds.getVariables().get(0);
List vl = cvs.getVariableList();
pw.println(" <Variables>");
for (int j = 0; j < vl.size(); j++) {
ThreddsMetadata.Variable v = (ThreddsMetadata.Variable) vl.get(j);
pw.println(
" <variable name=\""
+ v.getName()
+ "\" vocabulary_name=\""
+ v.getVocabularyName()
+ "\" units=\""
+ v.getUnits()
+ "\" />");
}
pw.println(" </Variables>");
String[] stations = rm.stationsDS(radarType, dataLocation.get(ds.getPath()));
rm.printStations(stations, pw, radarType);
pw.println(" </metadata>");
pw.println(" </dataset>");
}
pw.println("</catalog>");
pw.flush();
} catch (Throwable e) {
log.error("RadarServer.datasetInfoXml", e);
}
return;
}
public void doGet(HttpServletRequest request, HttpServletResponse response)
throws IOException, ServletException {
try {
response.setHeader("Cache-Control", "no-cache");
response.setCharacterEncoding("UTF-8");
String task = request.getParameter("task");
Element data = null;
// process help request
if (request.getParameter("help") != null) data = getDescription(task);
// redirect to home page if there is no task
if (data == null && task == null) {
response.setContentType("text/html");
response
.getWriter()
.append(
"<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\"><html><head><meta http-equiv=\"REFRESH\" content=\"0;url="
+ context.getInitParameter("server_path")
+ "></head><body></body></html>");
return;
}
// process definition request
if (data == null && task.equals("define")) {
int id = resolveIntegerArg(request.getParameter("id"), -1);
int length = resolveIntegerArg(request.getParameter("length"), definer.getDefaultLength());
int format = resolveIntegerArg(request.getParameter("format"), definer.getDefaultFormat());
int maxImageWidth =
resolveIntegerArg(
request.getParameter("maxImageWidth"), definer.getDefaultMaxImageWidth());
int maxImageHeight =
resolveIntegerArg(
request.getParameter("maxImageHeight"), definer.getDefaultMaxImageHeight());
int linkDestination =
resolveIntegerArg(
request.getParameter("linkDestination"), definer.getDefaultLinkDestination());
boolean getImages = resolveBooleanArg(request.getParameter("getImages"), false);
data =
definer.getDefinition(
id, length, format, linkDestination, getImages, maxImageWidth, maxImageHeight);
}
// all of the remaining tasks require data to be cached, so lets make sure that is finished
// before continuing.
if (!cachingThread.isOk()) throw new ServletException("Could not cache wikipedia data");
double progress = cachingThread.getProgress();
if (data == null && (progress < 1 || task.equals("progress"))) {
// still caching up data, not ready to return a response yet.
data = doc.createElement("loading");
data.setAttribute("progress", df.format(progress));
task = "loading";
}
// process search request
if (data == null && task.equals("search")) {
String term = request.getParameter("term");
String id = request.getParameter("id");
int linkLimit =
resolveIntegerArg(request.getParameter("linkLimit"), searcher.getDefaultMaxLinkCount());
int senseLimit =
resolveIntegerArg(
request.getParameter("senseLimit"), searcher.getDefaultMaxSenseCount());
if (id == null) data = searcher.doSearch(term, linkLimit, senseLimit);
else data = searcher.doSearch(Integer.parseInt(id), linkLimit);
}
// process compare request
if (data == null && task.equals("compare")) {
String term1 = request.getParameter("term1");
String term2 = request.getParameter("term2");
int linkLimit =
resolveIntegerArg(request.getParameter("linkLimit"), comparer.getDefaultMaxLinkCount());
boolean details =
resolveBooleanArg(request.getParameter("details"), comparer.getDefaultShowDetails());
data = comparer.getRelatedness(term1, term2, details, linkLimit);
}
// process wikify request
if (data == null && task.equals("wikify")) {
if (this.wikifier == null)
throw new ServletException(
"Wikifier is not available. You must configure the servlet so that it has access to link detection and disambiguation models.");
String source = request.getParameter("source");
int sourceMode =
resolveIntegerArg(request.getParameter("sourceMode"), Wikifier.SOURCE_AUTODETECT);
String linkColor = request.getParameter("linkColor");
String baseColor = request.getParameter("baseColor");
double minProb =
resolveDoubleArg(
request.getParameter("minProbability"), wikifier.getDefaultMinProbability());
int repeatMode =
resolveIntegerArg(request.getParameter("repeatMode"), wikifier.getDefaultRepeatMode());
boolean showTooltips =
resolveBooleanArg(
request.getParameter("showTooltips"), wikifier.getDefaultShowTooltips());
String bannedTopics = request.getParameter("bannedTopics");
boolean wrapInXml = resolveBooleanArg(request.getParameter("wrapInXml"), true);
if (wrapInXml) {
data =
wikifier.wikifyAndWrapInXML(
source,
sourceMode,
minProb,
repeatMode,
bannedTopics,
baseColor,
linkColor,
showTooltips);
} else {
response.setContentType("text/html");
response
.getWriter()
.append(
wikifier.wikify(
source,
sourceMode,
minProb,
repeatMode,
bannedTopics,
baseColor,
linkColor,
showTooltips));
return;
}
}
if (data == null) throw new Exception("Unknown Task");
// wrap data
Element wrapper = doc.createElement("WikipediaMinerResponse");
wrapper.setAttribute("server_path", context.getInitParameter("server_path"));
wrapper.setAttribute("service_name", context.getInitParameter("service_name"));
wrapper.appendChild(data);
data = wrapper;
// Transform or serialize xml data as appropriate
Transformer tf = null;
if (request.getParameter("xml") == null) {
// we need to transform the data into html
tf = transformersByName.get(task);
if (request.getParameter("help") != null) tf = transformersByName.get("help");
}
if (tf == null) {
// we need to serialize the data as xml
tf = transformersByName.get("serializer");
response.setContentType("application/xml");
} else {
// output will be transformed to html
response.setContentType("text/html");
response
.getWriter()
.append(
"<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">\n");
}
tf.transform(new DOMSource(data), new StreamResult(response.getWriter()));
} catch (Exception error) {
response.reset();
response.setContentType("application/xml");
response.setHeader("Cache-Control", "no-cache");
response.setCharacterEncoding("UTF8");
Element xmlError = doc.createElement("Error");
if (error.getMessage() != null) xmlError.setAttribute("message", error.getMessage());
Element xmlStackTrace = doc.createElement("StackTrace");
xmlError.appendChild(xmlStackTrace);
for (StackTraceElement ste : error.getStackTrace()) {
Element xmlSte = doc.createElement("StackTraceElement");
xmlSte.setAttribute("message", ste.toString());
xmlStackTrace.appendChild(xmlSte);
}
try {
transformersByName
.get("serializer")
.transform(new DOMSource(xmlError), new StreamResult(response.getWriter()));
} catch (Exception e) {
// TODO: something for when an error is thrown processing an error????
}
;
}
}
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;
}
public void _jspService(HttpServletRequest request, HttpServletResponse response)
throws java.io.IOException, ServletException {
JspFactory _jspxFactory = null;
PageContext pageContext = null;
HttpSession session = null;
Throwable exception = (Throwable) request.getAttribute("javax.servlet.jsp.jspException");
ServletContext application = null;
ServletConfig config = null;
JspWriter out = null;
Object page = this;
String _value = null;
try {
if (_jspx_inited == false) {
synchronized (this) {
if (_jspx_inited == false) {
_jspx_init();
_jspx_inited = true;
}
}
}
_jspxFactory = JspFactory.getDefaultFactory();
response.setContentType("text/html; charset=GBK");
pageContext =
_jspxFactory.getPageContext(this, request, response, "/error.jsp", true, 8192, true);
application = pageContext.getServletContext();
config = pageContext.getServletConfig();
session = pageContext.getSession();
out = pageContext.getOut();
// HTML // begin [file="/search/accountroleinfo.jsp";from=(2,96);to=(3,0)]
out.write("\r\n");
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(3,56);to=(4,0)]
out.write("\r\n");
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(4,55);to=(5,0)]
out.write("\r\n");
// end
// begin [file="/search/accountroleinfo.jsp";from=(5,0);to=(5,49)]
/* ---- power:checkpower ---- */
com.kingsoft.gmsystem.web.taglib.PowerTag _jspx_th_power_checkpower_0 =
new com.kingsoft.gmsystem.web.taglib.PowerTag();
_jspx_th_power_checkpower_0.setPageContext(pageContext);
_jspx_th_power_checkpower_0.setParent(null);
_jspx_th_power_checkpower_0.setModulecode("accountroleinfo");
try {
int _jspx_eval_power_checkpower_0 = _jspx_th_power_checkpower_0.doStartTag();
if (_jspx_eval_power_checkpower_0 == javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_BUFFERED)
throw new JspTagException(
"Since tag handler class com.kingsoft.gmsystem.web.taglib.PowerTag does not implement BodyTag, it can't return BodyTag.EVAL_BODY_TAG");
if (_jspx_eval_power_checkpower_0 != javax.servlet.jsp.tagext.Tag.SKIP_BODY) {
do {
// end
// begin [file="/search/accountroleinfo.jsp";from=(5,0);to=(5,49)]
} while (_jspx_th_power_checkpower_0.doAfterBody()
== javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_AGAIN);
}
if (_jspx_th_power_checkpower_0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE)
return;
} finally {
_jspx_th_power_checkpower_0.release();
}
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(5,49);to=(6,0)]
out.write("\r\n");
// end
// begin [file="/search/accountroleinfo.jsp";from=(6,2);to=(19,0)]
String account =
new String(Util.setNullToEmpty(request.getParameter("account")).getBytes("ISO-8859-1"));
String roleName =
new String(Util.setNullToEmpty(request.getParameter("roleName")).getBytes("ISO-8859-1"));
String zonecode = request.getParameter("zonecode2");
String game_code = request.getParameter("game_code");
String gatewayName = request.getParameter("gatewayName");
GMHelper gh = new GMHelper();
List gatewayList = gh.getGatewayList();
Iterator it = gatewayList.iterator();
Iterator accountRoleIterator = null;
if (null != request.getAttribute("accountRoleList"))
accountRoleIterator = ((ArrayList) request.getAttribute("accountRoleList")).iterator();
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(19,2);to=(27,14)]
out.write(
"\r\n<html>\r\n\t<!-- InstanceBegin template=\"/Templates/normal.dwt\" codeOutsideHTMLIsLocked=\"false\" -->\r\n\t<head>\r\n\t\t<meta http-equiv=\"Content-Type\" content=\"text/html; charset=GBK\">\r\n\t\t<!-- InstanceBeginEditable name=\"doctitle\" -->\r\n\t\t<title>玩家帐号角色互查</title>\r\n\t\t<!-- InstanceEndEditable -->\r\n\t\t<link href=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(27,17);to=(27,41)]
out.print(request.getContextPath());
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(27,43);to=(29,8)]
out.write(
"/css/public.css\" rel=\"stylesheet\" type=\"text/css\">\r\n\t\t<script language=\"JavaScript\"\r\n\t\t\tsrc=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(29,11);to=(29,35)]
out.print(request.getContextPath());
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(29,37);to=(31,16)]
out.write(
"/js/public.js\"></script>\r\n\t\t<script language=\"JavaScript\">\r\n\t\t\tvar AbsPath=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(31,19);to=(31,43)]
out.print(request.getContextPath());
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(31,45);to=(34,2)]
out.write(
"\"; \r\n\t\t</script>\r\n\t\t<!-- InstanceBeginEditable name=\"head\" -->\r\n\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(34,4);to=(34,4)]
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(34,6);to=(36,15)]
out.write("\r\n<script language=\"JavaScript\">\r\nvar game_code=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(36,18);to=(36,48)]
out.print(Util.setNullToEmpty(game_code));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(36,50);to=(37,14)]
out.write("\";\r\nvar zonecode=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(37,17);to=(37,46)]
out.print(Util.setNullToEmpty(zonecode));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(37,48);to=(38,18)]
out.write("\";\r\nvar gatewayNames=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(38,21);to=(38,53)]
out.print(Util.setNullToEmpty(gatewayName));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(38,55);to=(41,0)]
out.write("\";\r\nvar gatewayAry = new Array();\r\n\r\n");
// end
// begin [file="/search/accountroleinfo.jsp";from=(41,2);to=(49,0)]
HashMap hm = null;
int cnt = 0;
while (it.hasNext()) {
hm = (HashMap) it.next();
out.println(
"gatewayAry["
+ cnt++
+ "] =new Array('"
+ hm.get("game_id")
+ "','"
+ hm.get("zonecode")
+ "','"
+ hm.get("gateway_name")
+ "','"
+ hm.get("area")
+ "','"
+ hm.get("group")
+ "','"
+ hm.get("region")
+ "'); ");
}
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(49,2);to=(126,19)]
out.write(
"\r\n\r\nfunction checkValue()\r\n{\r\n\tvar strErr=\"\";\r\n\tif(IsEmpty(\"account\")&&IsEmpty(\"roleName\")) strErr+=\"*玩家帐号或角色信息不能同时为空\\n\";\r\n\tif(strErr!=\"\"){\r\n\t\talert(strErr);\t\r\n\t\treturn false;\r\n\t}else{\t\t\r\n\t\tvar objDiv = document.all(\"gateway\");\r\n\t\tvar aryCheck = objDiv.all.tags(\"INPUT\");\r\n\t\tvar intCheckLength = aryCheck.length;\r\n\t\tvar gateways = \"\";\r\n\t\tfor (i = 0; i < intCheckLength; i++) {\t\r\n\t\t\tif (aryCheck[i].checked) {\r\n\t\t\t\tgateways += aryCheck[i].name + \",\";\r\n\t\t\t}\r\n\t\t}\r\n\t\tdocument.all(\"gatewayName\").value = gateways;\r\n\t\treturn true;\r\n\t}\r\n}\r\n\r\nfunction onChangeGameId()\r\n{\r\n\tvar objSel=document.all(\"zonecode2\");\r\n\tvar objSelTemp=document.all(\"zonecodeTemp\");\r\n\tvar objOption;\r\n\tobjSel.length=0;\r\n\tvar j=0;\r\n\tfor(i=0;i<objSelTemp.length;i++)\r\n\t{\r\n\t\tobjOption=objSelTemp.options[i];\r\n\t\tif(objOption.game_id==document.all(\"game_code\").value)\r\n\t\t{\r\n\t\t \tj+=1;\r\n\t\t \tif(j==1){\r\n\t\t\tobjSel.options[objSel.length]=new Option(0+\".所有区\",'all');\r\n\t\t\tobjSel.options[objSel.length-1].setAttribute(\"game_id\",objOption.game_id);\r\n\t\t \t}\r\n\t\t\tobjSel.options[objSel.length]=new Option(j+\".\"+objOption.text,objOption.value);\r\n\t\t\tobjSel.options[objSel.length-1].setAttribute(\"game_id\",objOption.game_id);\r\n\t\t}\t\t\r\n\t}\r\n}\r\n</script>\r\n\t</head>\r\n\t<!-- InstanceEndEditable -->\r\n\r\n\t<body>\r\n\t\t<table width=\"100%\" height=\"100%\" border=\"0\" align=\"center\"\r\n\t\t\tcellspacing=\"0\">\r\n\t\t\t<tr>\r\n\t\t\t\t<td height=\"20\" bgcolor=\"#BBDDFD\">\r\n\t\t\t\t\t 当前位置：\r\n\t\t\t\t\t<!-- InstanceBeginEditable name=\"position\" -->\r\n\t\t\t\t\t<span class=\"title\">查询功能</span> >>\r\n\t\t\t\t\t<span class=\"title\">玩家帐号角色互查</span>\r\n\t\t\t\t\t<!-- InstanceEndEditable -->\r\n\t\t\t\t</td>\r\n\t\t\t</tr>\r\n\t\t\t<tr>\r\n\t\t\t\t<td align=\"center\" valign=\"top\">\r\n\t\t\t\t\t<!-- InstanceBeginEditable name=\"main\" -->\r\n\t\t\t\t\t<div id=\"divPrompt\"\r\n\t\t\t\t\t\tstyle=\"width: 250px; position: absolute; display: none; left: 340px; top: 300px; height: 44px;\">\r\n\t\t\t\t\t\t<table width=\"100%\" height=\"100%\" border=\"1\" align=\"center\"\r\n\t\t\t\t\t\t\tcellspacing=\"0\" bordercolor=\"#0000FF\" bgcolor=\"#FFFFFF\">\r\n\t\t\t\t\t\t\t<tr>\r\n\t\t\t\t\t\t\t\t<td align=\"center\" valign=\"middle\">\r\n\t\t\t\t\t\t\t\t\t正在查询和等待返回结果，请稍候......\r\n\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t</tr>\r\n\t\t\t\t\t\t</table>\r\n\t\t\t\t\t</div>\r\n\t\t\t\t\t<br>\r\n\t\t\t\t\t<form action=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(126,22);to=(126,46)]
out.print(request.getContextPath());
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(126,48);to=(139,8)]
out.write(
"/GMCServlet?action=accountroleinfo\" method=\"post\" onsubmit=\"return checkValue()\">\r\n\t\t\t\t\t<table width=\"100%\" border=\"0\" cellspacing=\"0\">\r\n\t\t\t\t\t\t<tr>\r\n\t\t\t\t\t\t\t<td align=\"center\">\r\n\t\t\t\t\t\t\t\t所属游戏\r\n\t\t\t\t\t\t\t\t<select id=\"selectGamename\" name=\"game_code\"\r\n\t\t\t\t\t\t\t\t\tonmouseover=\"this.focus()\" onchange=\"onChangeGameId()\">\r\n\t\t\t\t\t\t\t\t\t<OPTION value='88'>\r\n\t\t\t\t\t\t\t\t\t\t剑网3\r\n\t\t\t\t\t\t\t\t\t</OPTION>\r\n\t\t\t\t\t\t\t\t</select>\r\n\t\t\t\t\t\t\t\t所在区\r\n\t\t\t\t\t\t\t\t<select name=\"zonecode2\"></select>\r\n\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(139,8);to=(140,58)]
/* ---- display:display ---- */
com.kingsoft.gmsystem.web.taglib.UserTag _jspx_th_display_display_0 =
new com.kingsoft.gmsystem.web.taglib.UserTag();
_jspx_th_display_display_0.setPageContext(pageContext);
_jspx_th_display_display_0.setParent(null);
_jspx_th_display_display_0.setDisplayCode("select_zone_all");
_jspx_th_display_display_0.setProperty("zonecodeTemp");
_jspx_th_display_display_0.setParameter("display:none");
try {
int _jspx_eval_display_display_0 = _jspx_th_display_display_0.doStartTag();
if (_jspx_eval_display_display_0 == javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_BUFFERED)
throw new JspTagException(
"Since tag handler class com.kingsoft.gmsystem.web.taglib.UserTag does not implement BodyTag, it can't return BodyTag.EVAL_BODY_TAG");
if (_jspx_eval_display_display_0 != javax.servlet.jsp.tagext.Tag.SKIP_BODY) {
do {
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(140,58);to=(141,8)]
out.write("\r\n\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(141,8);to=(141,26)]
} while (_jspx_th_display_display_0.doAfterBody()
== javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_AGAIN);
}
if (_jspx_th_display_display_0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) return;
} finally {
_jspx_th_display_display_0.release();
}
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(141,26);to=(149,16)]
out.write(
"\r\n\t\t\t\t\t\t\t\t<input type=\"hidden\" name=\"gatewayName\"/>\r\n\t\t\t\t\t\t\t\t所在服\r\n\t\t\t\t\t\t\t\t<div id=\"gateway\">\r\n\t\t\t\t\t\t\t\t</div>\r\n\r\n\t\t\t\t\t\t\t\t玩家帐号\r\n\t\t\t\t\t\t\t\t<input name=\"account\" type=\"text\" class=\"text\"\r\n\t\t\t\t\t\t\t\t\tvalue=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(149,19);to=(149,26)]
out.print(account);
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(149,28);to=(152,63)]
out.write(
"\" onmouseover=\"this.focus()\" size=\"20\"\r\n\t\t\t\t\t\t\t\t\tmaxlength=\"30\">\r\n\t\t\t\t\t\t\t\t玩家角色\r\n\t\t\t\t\t\t\t\t<input type=\"text\" name=\"roleName\" class=\"text\" value=\"");
// end
// begin [file="/search/accountroleinfo.jsp";from=(152,66);to=(152,74)]
out.print(roleName);
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(152,76);to=(154,45)]
out.write(
"\"\r\n\t\t\t\t\t\t\t\t\tonmouseover=\"this.focus()\" size=\"20\" maxlength=\"30\">\r\n\t\t\t\t\t\t\t\t<input type=\"checkbox\" name=\"isLike\" ");
// end
// begin [file="/search/accountroleinfo.jsp";from=(154,48);to=(154,128)]
out.print(Util.setNullToEmpty(request.getParameter("isLike")).equals("") ? "" : "checked");
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(154,130);to=(183,9)]
out.write(
">模糊查询\r\n\t\t\t\t\t\t\t\t<input type=\"submit\" name=\"btnSearch\" value=\"查询\"/>\t\t\t\t\t\t\t\t\r\n\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t</tr>\r\n\t\t\t\t\t\t<tr>\r\n\t\t\t\t\t\t\t<td align=\"center\">\r\n\t\t\t\t\t\t\t\t<br>\r\n\t\t\t\t\t\t\t\t<table width=\"773\" border=\"1\" cellpadding=\"0\" cellspacing=\"0\"\r\n\t\t\t\t\t\t\t\t\tclass=\"tablelist\">\r\n\t\t\t\t\t\t\t\t\t<tr align=\"left\" bgcolor=\"#419ADC\">\r\n\t\t\t\t\t\t\t\t\t\t<td height=\"31\" colspan=\"6\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t<font color=#ffffff><b> • 玩家帐号基本信息</b>\r\n\t\t\t\t\t\t\t\t\t\t\t</font>\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t</tr>\r\n\t\t\t\t\t\t\t\t\t<tr>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t玩家帐号\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t玩家角色\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t所在区\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t所在服\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t</tr>\r\n\t\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(183,11);to=(187,9)]
if (null != accountRoleIterator) {
while (accountRoleIterator.hasNext()) {
hm = (HashMap) accountRoleIterator.next();
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(187,11);to=(191,11)]
out.write(
"\r\n\t\t\t\t\t\t\t\t\t\r\n\t\t\t\t\t\t\t\t\t<tr>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(191,14);to=(191,32)]
out.print(hm.get("account"));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(191,34);to=(194,11)]
out.write(
"\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(194,14);to=(194,33)]
out.print(hm.get("RoleName"));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(194,35);to=(197,11)]
out.write(
"\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(197,14);to=(197,33)]
out.print(hm.get("ZoneName"));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(197,35);to=(200,11)]
out.write(
"\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t\t<td width=\"25%\" height=\"25\" align=\"right\" nowrap>\r\n\t\t\t\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(200,14);to=(200,36)]
out.print(hm.get("GatewayName"));
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(200,38);to=(203,9)]
out.write(
"\r\n\t\t\t\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t\t\t\t</tr>\r\n\t\t\t\t\t\t\t\t\t");
// end
// begin [file="/search/accountroleinfo.jsp";from=(203,11);to=(206,9)]
}
}
// end
// HTML // begin [file="/search/accountroleinfo.jsp";from=(206,11);to=(260,0)]
out.write(
"\r\n\t\t\t\t\t\t\t\t</table>\r\n\t\t\t\t\t\t\t</td>\r\n\t\t\t\t\t\t</tr>\r\n\t\t\t\t\t</table>\r\n\t\t\t\t\t</form>\r\n\t\t\t\t\t<script language=\"JavaScript\">\r\ndocument.getElementById(\"zonecode2\").onchange = function onChangeZoneCode(){\r\n\tvar objSel = document.getElementById(\"zonecode2\");\r\n\tvar objOpt = objSel.options[objSel.selectedIndex];\r\n\tvar tmp = \"\";\r\n\tfor(var cnt=0;cnt<gatewayAry.length;cnt++){\r\n\t\tif(gatewayAry[cnt][0]==objOpt.game_id&&gatewayAry[cnt][1]==objOpt.value){\t\r\n\t\t\ttmp +=\" <input type='checkbox' name='\"+gatewayAry[cnt][5]+\"'>\"+gatewayAry[cnt][2];\r\n\t\t}\r\n\t}\r\n\tdocument.getElementById(\"gateway\").innerHTML = tmp;\r\n}\r\n\r\n\t if(game_code!=\"\"){\r\n\t\tSetSelValue(\"game_code\",game_code);\r\n onChangeGameId();\r\n SetSelValue(\"zonecode2\",zonecode);\r\n\t }else{\r\n onChangeGameId();\r\n }\r\n if(zonecode!=\"\"){\r\n\t\tonChangeZoneCode();\r\n\t\tif(gatewayNames!=\"\"){\r\n\t\t\tvar objDiv = document.all(\"gateway\");\r\n\t\t\tvar aryCheck = objDiv.all.tags(\"INPUT\");\r\n\t\t\tvar intCheckLength = aryCheck.length;\r\n\t\t\tvar gateways = \"\";\r\n\t\t\tfor (i = 0; i < intCheckLength; i++) {\t\r\n\t\t\t\tif (gatewayNames.indexOf(aryCheck[i].name+\",\")>-1) {\r\n\t\t\t\t\taryCheck[i].checked=true;\r\n\t\t\t\t}\r\n\t\t\t}\r\n\t\t}\t\t\r\n\t\t\r\n \t }\r\n\t</script>\r\n\t\t\t\t\t<!-- InstanceEndEditable -->\r\n\t\t\t\t</td>\r\n\t\t\t</tr>\r\n\t\t\t<tr>\r\n\t\t\t\t<td height=\"16\" align=\"center\" bgcolor=\"#BBDDFD\">\r\n\t\t\t\t\tCopyright © 2005 Kingsoft Corp,All Rights Reserved\r\n\t\t\t\t</td>\r\n\t\t\t</tr>\r\n\t\t</table>\r\n\t</body>\r\n\t<!-- InstanceEnd -->\r\n</html>\r\n");
// end
} catch (Throwable t) {
if (out != null && out.getBufferSize() != 0) out.clearBuffer();
if (pageContext != null) pageContext.handlePageException(t);
} finally {
if (_jspxFactory != null) _jspxFactory.releasePageContext(pageContext);
}
}
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.");
}
}
/**
* 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();
}
}