List of usage examples for java.lang Exception getStackTrace
public StackTraceElement[] getStackTrace()
From source file:org.alfresco.reporting.processor.NodeRefBasedPropertyProcessor.java
@Override protected ReportLine processNodeToMap(String identifier, String table, ReportLine rl) { table = dbhb.fixTableColumnName(table); if (logger.isDebugEnabled()) logger.debug("processNodeToMap, identifier=" + identifier); NodeRef masterRef = null;/*from w w w .j av a2 s . c o m*/ NodeRef nodeRef = new NodeRef(identifier.split(",")[0]); if (identifier.contains(",")) { masterRef = new NodeRef(identifier.split(",")[1]); } // NodeRef nodeRef=new NodeRef(identifier); if (logger.isDebugEnabled()) logger.debug("Enter processNodeToMap nodeRef=" + nodeRef); try { // logger.debug("processNodeToMap: processing values"); rl = processPropertyValues(rl, nodeRef); } catch (Exception e) { // logger.error("processprocessNodeToMap: That is weird, // processPropertyValues crashed! " + nodeRef); e.printStackTrace(); } try { rl = processAssociationValues(rl, nodeRef); } catch (Exception e) { // logger.error("processNodeToMap: That is weird, // processAssociationValues crashed! " + nodeRef); e.printStackTrace(); } try { rl.setLine(Constants.COLUMN_NODEREF, getClassToColumnType().getProperty("noderef"), nodeRef.toString(), getReplacementDataType()); } catch (Exception e) { // logger.error("processNodeToMap: That is weird, // rl.setLine(noderef) crashed! " + nodeRef); e.printStackTrace(); } try { String typeString = nodeService.getType(nodeRef).getLocalName(); // .getPrefixedQName(resolver);// // apparently for native documents (cm:content) the type == null. // Code below should fix if (typeString == null) { typeString = nodeService.getType(nodeRef).toString(); typeString = typeString.substring(typeString.lastIndexOf(":")); } rl.setLine(Constants.COLUMN_OBJECT_TYPE, getClassToColumnType().getProperty(Constants.COLUMN_OBJECT_TYPE, ""), typeString, getReplacementDataType()); } catch (Exception e) { // it does not have a type (??). Bad luck. Don't crash // (versionStore?!) logger.debug("EXCPTION1: // it does not have a Type. Bad luck. Don't crash (versionStore?!)"); e.printStackTrace(); } String aspectString = ""; try { Set<QName> aspectsSet = nodeService.getAspects(nodeRef); Iterator<QName> aspectIterator = aspectsSet.iterator(); while (aspectIterator.hasNext()) { QName aspect = aspectIterator.next(); if (aspectString.length() > 0) { aspectString += ","; } aspectString += aspect.getLocalName(); // getPrefixedQName(resolver);// // getLocalName(); } // end while rl.setLine(Constants.COLUMN_ASPECTS, getClassToColumnType().getProperty(Constants.COLUMN_ASPECTS, ""), aspectString, getReplacementDataType()); } catch (Exception e) { // it does not have aspects. Bad luck. Don't crash (versionStore?!) // logger.debug("EXCPTION1: // it does not have Aspects. Bad luck. // Don't crash (versionStore?!)"); e.printStackTrace(); } Path path; String displayPath = ""; try { path = getNodeService().getPath(nodeRef); displayPath = toDisplayPath(path); rl.setLine(Constants.COLUMN_PATH, getClassToColumnType().getProperty(Constants.COLUMN_PATH), displayPath, getReplacementDataType()); } catch (Exception e) { // it does not have a path. Bad luck. Don't crash (versionStore?!) // logger.debug("EXCPTION1: // it is not in a site. Bad luck. Don't // crash (versionStore?!)"); e.printStackTrace(); } String site = ""; try { site = getSiteName(nodeRef); rl.setLine(Constants.COLUMN_SITE, getClassToColumnType().getProperty(Constants.COLUMN_SITE), site, getReplacementDataType()); } catch (Exception e) { // it is not in a site. Bad luck. Don't crash } QName myType = getNodeService().getType(nodeRef); if (getDictionaryService().isSubClass(myType, ContentModel.TYPE_FOLDER)) { NodeRef origNodeRef = null; try { if (nodeRef.toString().startsWith(StoreRef.PROTOCOL_ARCHIVE)) { ChildAssociationRef car = (ChildAssociationRef) nodeService.getProperty(nodeRef, QName.createQName("http://www.alfresco.org/model/system/1.0", "archivedOriginalParentAssoc")); logger.debug("ORIGIN: child:" + car.getChildRef() + " parent: " + car.getParentRef()); origNodeRef = car.getChildRef(); } } catch (Exception e) { logger.fatal("Exception getting orig_noderef" + e.getStackTrace()); } if (origNodeRef != null) { // it is an archived thingy if (logger.isDebugEnabled()) logger.debug("Setting Ref from archive to orig_noderef!!!"); rl.setLine(Constants.COLUMN_ORIG_NODEREF, getClassToColumnType().getProperty("noderef"), origNodeRef.toString(), getReplacementDataType()); } else { if (logger.isDebugEnabled()) logger.debug("Setting currentRef to orig_noderef!!!"); rl.setLine(Constants.COLUMN_ORIG_NODEREF, getClassToColumnType().getProperty("noderef"), nodeRef.toString(), getReplacementDataType()); } } if (getDictionaryService().isSubClass(myType, ContentModel.TYPE_CONTENT) || (getDictionaryService().getType(myType)).toString() .equalsIgnoreCase(ContentModel.TYPE_CONTENT.toString())) { long size = 0; String sizeString = "0"; try { size = getFileFolderService().getFileInfo(nodeRef).getContentData().getSize(); if (size == 0) { sizeString = "0"; } else { sizeString = Long.toString(size); } // get the COLUMN_SIZE prop, being "size" for MySQL, but // "docsize" for Oracle rl.setLine(COLUMN_SIZE, getClassToColumnType().getProperty(COLUMN_SIZE), sizeString, getReplacementDataType()); } catch (Exception e) { logger.info("processNodeToMap: Huh, no size?"); sizeString = "0"; } boolean versioned = false; try { versioned = getNodeService().hasAspect(nodeRef, ContentModel.ASPECT_VERSIONABLE); rl.setLine("versioned", getClassToColumnType().getProperty("boolean"), String.valueOf(versioned), getReplacementDataType()); } catch (Exception e) { logger.info("processNodeToMap: Huh, no versioned info?"); e.printStackTrace(); } try { String mimetype = getFileFolderService().getFileInfo(nodeRef).getContentData().getMimetype(); if (mimetype == null) mimetype = "NULL"; rl.setLine(Constants.COLUMN_MIMETYPE, getClassToColumnType().getProperty(Constants.COLUMN_MIMETYPE), mimetype, getReplacementDataType()); } catch (Exception e) { logger.info("processNodeToMap: Huh, no mimetype?"); } NodeRef origNodeRef = null; try { if (nodeRef.toString().startsWith(StoreRef.PROTOCOL_ARCHIVE)) { ChildAssociationRef car = (ChildAssociationRef) nodeService.getProperty(nodeRef, QName.createQName("http://www.alfresco.org/model/system/1.0", "archivedOriginalParentAssoc")); logger.debug("ORIGIN: child:" + car.getChildRef() + " parent: " + car.getParentRef()); origNodeRef = car.getChildRef(); } } catch (Exception e) { logger.warn("Exception getting orig_noderef" + e.getStackTrace()); } try { if (nodeRef.toString().startsWith("version")) { // replace all archive-space references in the orig_noderef // into the workspace one. if (logger.isDebugEnabled()) { logger.debug("Setting nodeRef to orig_noderef - VERSION!!!"); logger.debug("Master says: " + masterRef.toString()); } rl.setLine(Constants.COLUMN_ORIG_NODEREF, getClassToColumnType().getProperty("noderef"), masterRef.toString(), getReplacementDataType()); } else { if (origNodeRef != null) { // it is an archived thingy if (logger.isDebugEnabled()) logger.debug("Setting Ref from archive to orig_noderef!!!"); rl.setLine(Constants.COLUMN_ORIG_NODEREF, getClassToColumnType().getProperty("noderef"), origNodeRef.toString(), getReplacementDataType()); } else { if (logger.isDebugEnabled()) logger.debug("Setting currentRef to orig_noderef!!!"); rl.setLine(Constants.COLUMN_ORIG_NODEREF, getClassToColumnType().getProperty("noderef"), nodeRef.toString(), getReplacementDataType()); } } } catch (Exception e) { // don't crash... (versionStore?!) // logger.debug("EXCPTION: don't crash... (versionStore?!)"); } } // end if else { if (logger.isDebugEnabled()) logger.debug(myType.toString() + " is no content subclass!"); } return rl; }
From source file:ru.apertum.qsystem.client.forms.FAdmin.java
@Action
public void saveConfiguration() {
saveNet();/*ww w.jav a 2s . c o m*/
final Exception res;
try {
res = (Exception) Spring.getInstance().getTt().execute(new TransactionCallback() {
@Override
public Exception doInTransaction(TransactionStatus status) {
try {
//? ? ?
Spring.getInstance().getHt().saveOrUpdate(ServerProps.getInstance().getProps());
//?
Spring.getInstance().getHt().saveOrUpdate(ServerProps.getInstance().getStandards());
// ? ???
QScheduleList.getInstance().save();
// ? ??
QBreaksList.getInstance().save();
// ? ?
QCalendarList.getInstance().save();
// ? ?
QServiceTree.getInstance().save();
// ?
QUserList.getInstance().save();
// ?
QInfoTree.getInstance().save();
// ?
QResponseList.getInstance().save();
// ? ? ?
QResultList.getInstance().save();
QLog.l().logger().debug(" .");
} catch (Exception ex) {
QLog.l().logger().error(" ? \n" + ex.toString() + "\n"
+ Arrays.toString(ex.getStackTrace()));
status.setRollbackOnly();
return ex;
}
return null;
}
});
} catch (RuntimeException ex) {
throw new ClientException(
" ? ? (JDBC). ?.\n("
+ ex.toString() + ")");
}
if (res == null) {
JOptionPane.showMessageDialog(this, getLocaleMessage("admin.save.title"),
getLocaleMessage("admin.save.caption"), JOptionPane.INFORMATION_MESSAGE);
} else {
throw new ClientException(
" ? ? (JDBC). ?.\n["
+ res.getLocalizedMessage() + "]\n(" + res.toString() + ")\nSQL: ");
}
}
From source file:edu.cornell.mannlib.vitro.webapp.controller.edit.RefactorOperationController.java
private String doFixDataTypes(HttpServletRequest request, HttpServletResponse response) { try {//from w w w. j a va2s . com super.doGet(request, response); } catch (Exception e) { log.error(this.getClass().getName() + " caught exception calling doGet()"); } VitroRequest vreq = new VitroRequest(request); RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP); request.setAttribute("bodyJsp", Controllers.CHECK_DATATYPE_PROPERTIES); request.setAttribute("title", "Check Datatype Properties"); request.setAttribute("css", "<link rel=\"stylesheet\" type=\"text/css\" href=\"" + vreq.getAppBean().getThemeDir() + "css/edit.css\"/>"); OntModel ontModel = ModelAccess.on(getServletContext()).getOntModel(FULL_ASSERTIONS); ontModel.enterCriticalSection(Lock.WRITE); ArrayList<String> results = new ArrayList<String>(); try { ExtendedIterator dataProperties = ontModel.listDatatypeProperties(); int hasRange = 0; int consistent = 0; int inconsistent = 0; int total = 0; int fixed = 0; while (dataProperties.hasNext()) // Iterate through all datatype properties { total++; DatatypeProperty p = (DatatypeProperty) dataProperties.next(); OntResource range = p.getRange(); if (range != null) hasRange++; NodeIterator n = ontModel.listObjectsOfProperty(p); //if(!n.hasNext()) results.add(p.getLocalName()+" is not in any statements"); while (n.hasNext()) // Iterate through all objects of all datatype properties { RDFNode node = n.nextNode(); if (node.isLiteral()) { if (range != null) // If a literal has a predicate with a defined range, check and fix the literal's datatype { Literal l = (Literal) node; StmtIterator usingPandL = ontModel.listStatements(null, p, l); int size = 0; results.add("Statements using property " + p.getLocalName() + " and literal " + l.getLexicalForm() + ":"); while (usingPandL.hasNext()) { Statement st = usingPandL.nextStatement(); results.add(" " + st.getSubject().getLocalName() + " " + p.getLocalName() + " " + l.getLexicalForm()); size++; } usingPandL.close(); boolean valid = range.getURI().equals(l.getDatatypeURI()); if (valid) consistent += size; else { results.add(p.getLocalName() + " has object " + l.getLexicalForm() + " of type " + l.getDatatypeURI() + " which is inconsistent"); String typeName = ""; if (range.getURI().contains(XSDDatatype.XSD)) typeName = range.getURI().substring(XSDDatatype.XSD.length() + 1); else results.add("ERROR: " + p.getLocalName() + " has a range which does not contain the XSD namespace"); Literal newLiteral = null; try { newLiteral = ontModel.createTypedLiteral(l.getLexicalForm(), new XSDDatatype(typeName)); } catch (NullPointerException e) { results.add( "ERROR: Can't create XSDDatatype for literal " + l.getLexicalForm()); } StmtIterator badStatements = ontModel.listStatements(null, p, l); StmtIterator toRemove = ontModel.listStatements(null, p, l); ArrayList<Statement> queue = new ArrayList<Statement>(); while (badStatements.hasNext()) { Statement badState = badStatements.nextStatement(); Statement goodState = ontModel.createStatement(badState.getSubject(), p, newLiteral); queue.add(goodState); results.add(" Replacing: " + badState.toString()); results.add(" With: " + goodState.toString()); fixed++; } for (int i = 0; i < queue.size(); i++) { ontModel.add(queue.get(i)); } ontModel.remove(toRemove); badStatements.close(); toRemove.close(); } if (valid) results.add("Literal " + l.getLexicalForm() + " is in the range of property " + p.getLocalName()); results.add("--------------"); } } else results.add("ERROR: " + node.toString() + " is not a literal"); } n.close(); } dataProperties.close(); results.add(hasRange + " of " + total + " datatype properties have defined ranges."); results.add("Of the statements that contain datatype properties with defined ranges, " + consistent + " are consistent and " + fixed + " are inconsistent."); results.add(fixed + " statements have been fixed."); //for(int i=0; i<results.size(); i++) System.out.println(results.get(i)); } finally { ontModel.leaveCriticalSection(); } request.setAttribute("results", results); try { rd.forward(request, response); } catch (Exception e) { log.error(this.getClass().getName() + " could not forward to view."); log.error(e.getMessage()); log.error(e.getStackTrace()); } return ""; }
From source file:com.inverse2.ajaxtoaster.AjaxToasterServlet.java
/** * Processes requests from the client for both HTTP <code>GET</code> * and <code>POST</code> methods. * * @param request servlet request/*from w w w. j a v a 2 s . c om*/ * @param response servlet response */ protected void processRequest(String requestType, HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { String responseFormat = response_format_prop; // flags that the user has not set the response format boolean defaultResponseFormat = response_format_prop.equals("XML") ? true : false; ServiceOperationInterface service = null; String callbackFunction = null; log.info(">> Start processRequest(" + requestType + ") at " + new Date()); try { ServletContext context = getServletContext(); String scriptName = request.getParameter(PARAM_SCRIPTNAME1); // look for "service=xxxx" String contextPath = ""; /* If the service parameter is not specified then use the URL to get the service name... */ if (scriptName == null) { scriptName = request.getPathInfo(); contextPath = request.getContextPath(); /* //Put this in for debugging... System.out.println("****** -> pathInfo [" + request.getPathInfo() + "]"); System.out.println("****** -> pathTranslated [" + request.getPathTranslated() + "]"); System.out.println("****** -> contextPath [" + request.getContextPath() + "]"); System.out.println("****** -> localAddr [" + request.getLocalAddr() + "]"); System.out.println("****** -> localName [" + request.getLocalName() + "]"); System.out.println("****** -> requestURI [" + request.getRequestURI() + "]");//***** System.out.println("****** -> servletPath [" + request.getServletPath() + "]"); */ if (scriptName == null) { scriptName = "UNSPECIFIED_SERVICE"; } } /* See if the URI is mapped to another service... */ ServiceMapping serviceMapping; serviceMapping = serviceMapper.getURIMapping(""/*contextPath*/, scriptName, requestType); if (serviceMapping != null) { log.info("Redirect URI to [" + serviceMapping.getServiceName() + "]"); scriptName = serviceMapping.getServiceName(); /* If the URI has been mapped then see if the "Accept" header specifies the return type required... */ String accept = request.getHeader("Accept"); if (accept.indexOf("text/xml") != -1) { responseFormat = "XML"; defaultResponseFormat = false; } if (accept.indexOf("text/json") != -1) { responseFormat = "JSON"; defaultResponseFormat = false; } } if (scriptName.startsWith("/")) { scriptName = scriptName.substring(1, scriptName.length()); } /** * If "log" service invoked then process it... */ if (scriptName.equals("log")) { returnHTMLLog(response); return; } /** * If "health" service invoked then process it... */ if (scriptName.equals("health")) { returnHealth(response); return; } /* Check for the flag to return XML or JSON objects... */ if (request.getParameter(PARAM_RETURNXML) != null) { println(">> Servlet will return XML object."); responseFormat = "XML"; defaultResponseFormat = false; } else if (request.getParameter(PARAM_RETURNJSON) != null) { println(">> Servlet will return XML object."); responseFormat = "JSON"; defaultResponseFormat = false; } else if (request.getParameter(PARAM_RETURNRAW) != null) { println(">> Servlet will return raw text object."); responseFormat = "RAW"; defaultResponseFormat = false; } /* Check for the callback function parameter... */ callbackFunction = request.getParameter(PARAM_CALLBACK); /** * Check to see if the client wants a "Service Mapping Description" (SMD) for the 'service'... */ if (request.getParameter(PARAM_SMD) != null) { log.info("Client wants SMD for [" + scriptName + "]"); try { ServicePool pool = null; Map availableServices = null; ServiceMappingDescription smd = null; ServiceScriptPool serviceScriptPool = null; String serviceScriptName = null; String returnString = null; pool = (ServicePool) context.getAttribute(ATTRIB_SERVICE_POOL); availableServices = pool.getAvailableServices(); smd = new ServiceMappingDescription(request.getRequestURL().toString(), request.getRequestURL().toString() + "?smd", null); for (Iterator it = availableServices.values().iterator(); it.hasNext();) { serviceScriptPool = (ServiceScriptPool) it.next(); serviceScriptName = serviceScriptPool.getPoolName(); /** * If the service script name begins with the passed in script name then add it to the * service mapping description... */ log.debug("scriptName = [" + scriptName + "], serviceScriptName = [" + serviceScriptName + "]"); if (scriptName.equals("") || serviceScriptName.startsWith(scriptName + "/") || serviceScriptName.equals(scriptName)) { smd.addOperation(serviceScriptName); service = serviceScriptPool.getService(); smd.setOperationDescription(service.getScriptDescription()); smd.setOperationTransport(service.getHTTPMethods()); smd.setOperationEnvelope("URL"); smd.setOperationContentType(service.getResponseFormat()); smd.setOperationParameters(serviceScriptPool.getServiceParameters()); smd.setOperationReturns(serviceScriptPool.getServiceReturns()); } } returnString = smd.getSMDJSONString(); writeResponse(returnString, "JSONRAW", callbackFunction, response); } catch (Exception ex) { log.error("Exception getting SMD: " + ex.toString()); ex.printStackTrace(); } return; } /** * Get the service and run it... */ println(">> Client wants to invoke the service [" + scriptName + "]"); try { service = getServiceScript(scriptName); } catch (Exception ex) { errorResponse(response, "Could not get an instance of the service [" + scriptName + "]: " + ex.toString(), responseFormat, callbackFunction); return; } if (service == null) { errorResponse(response, "Service [" + scriptName + "] not found.", responseFormat, callbackFunction); return; } /** * If the script exists in the toaster pool then invoke it */ println(">> Checking login required"); try { if (service.getLoginRequired().equals("true")) { HttpSession session = request.getSession(false); Object loggedIn = null; if (session != null) { loggedIn = session.getAttribute(ATTRIB_LOGGED_IN); } log.trace("**** SESSION = " + session); log.trace("**** Logged In = " + loggedIn); if (session == null || loggedIn == null || loggedIn.equals("true") == false) { errorResponse(response, "The service " + scriptName + " requires you to be logged in to run it.", responseFormat, callbackFunction); freeServiceScript(service); return; } /* Check that the logged in user is authorised to run the service... */ String validUsers; String[] validUsersArray; String user; String loggedInUser; boolean validUser; validUsers = service.getValidUsers(); validUsersArray = validUsers.split("[,]"); loggedInUser = (String) session.getAttribute(ATTRIB_LOGGED_IN_USER); validUser = false; for (int idx = 0; idx < validUsersArray.length; idx++) { user = validUsersArray[idx].trim(); if (user.equals("*")) { validUser = true; break; } if (user.equals(loggedInUser)) { validUser = true; break; } } if (validUser == false) { log.error("The user [" + loggedInUser + "] is not authorised to invoke the service [" + scriptName + "]"); errorResponse(response, "You are not authorised to invoke the service [" + scriptName + "]", responseFormat, callbackFunction); freeServiceScript(service); return; } } } catch (Exception ex) { errorResponse(response, "Could not check if login required for this service. " + ex.toString(), responseFormat, callbackFunction); return; } boolean scriptInputSet = false; /* * Go through the set of parameters passed to us and set them up in the service instance... */ for (Enumeration e = request.getParameterNames(); e.hasMoreElements();) { String parameterName = (String) e.nextElement(); if (parameterName.equals(PARAM_SCRIPTNAME1) == true || parameterName.equals(PARAM_SCRIPTNAME2) == true || parameterName.equals(PARAM_RETURNXML) == true || parameterName.equals(PARAM_RETURNJSON) == true || parameterName.equals(PARAM_CALLBACK) == true) { continue; } String parameterValue = (String) request.getParameter(parameterName); if (parameterName.equals(PARAM_INPUTXML) == true) { service.setInputXML(parameterValue); scriptInputSet = true; continue; } if (parameterName.equals(PARAM_INPUTJSON) == true) { try { // The input object is a JSON object... so convert it into XML... JSONObject json = new JSONObject(parameterValue); service.setInputXML(XML.toString(json)); scriptInputSet = true; println("JSON converted to \n" + XML.toString(json)); } catch (JSONException ex) { errorResponse(response, "Could not create JSON object." + ex.toString() + ". " + ex.getStackTrace(), responseFormat, callbackFunction); freeServiceScript(service); return; } continue; } /* Any leftover parameters are query parameters. */ println("Query Parameter found... Setting " + parameterName + " to " + parameterValue); service.setParameter(parameterName, parameterValue); } // End of parameters for loop /* If there is content in the request then, unless we have already set it, this is the input to the script... */ if (requestType.equals("POST") && scriptInputSet == false) { try { BufferedReader reader = request.getReader(); StringBuffer buf = new StringBuffer(); String line; String postData; while ((line = reader.readLine()) != null) { buf.append(line); } postData = buf.toString(); log.debug("POST DATA: " + postData); if (postData.startsWith("<")) { service.setInputXML(postData); scriptInputSet = true; } else { try { // The input object is a JSON object... so convert it into XML... JSONObject json = new JSONObject(postData); service.setInputXML(XML.toString(json)); scriptInputSet = true; log.debug("POST JSON converted to \n" + XML.toString(json)); } catch (JSONException ex) { errorResponse(response, "Could not convert POSTed JSON object." + ex.toString() + ". " + ex.getStackTrace(), responseFormat, callbackFunction); freeServiceScript(service); return; } } } catch (Exception ex) { log.warn("Exception getting posted data: " + ex.toString()); errorResponse(response, "Could not convert posted data.", responseFormat, callbackFunction); freeServiceScript(service); return; } } /* If the service name has been redirected then set any parameters that where embedded in the URI... */ if (serviceMapping != null) { Properties serviceParameters = serviceMapping.getParameters(); String paramName; String paramValue; for (Enumeration<Object> en = serviceParameters.keys(); en.hasMoreElements();) { paramName = (String) en.nextElement(); paramValue = (String) serviceParameters.get(paramName); service.setParameter(paramName, paramValue); } } String serviceResultString = null; /** * Run the service script... */ service.setSessionRequest(request); service.setSessionResponse(response); service.setCallbackFunction(callbackFunction); /* Check if the service has a predefined output format... */ /* If the user has specified a format then that is used.. */ String operationResponseFormat; operationResponseFormat = service.getResponseFormat(); if (defaultResponseFormat == true && operationResponseFormat != null && operationResponseFormat.equals("") == false) { responseFormat = operationResponseFormat; } service.setInvokeResponseFormat(responseFormat); /* If this is a priviledged operation then pass in a reference to the servlet... */ String priviledgedOperation = service.getPriviledged(); if (priviledgedOperation.compareToIgnoreCase("true") == 0 || priviledgedOperation.compareToIgnoreCase("yes") == 0 || priviledgedOperation.compareToIgnoreCase("y") == 0) { service.setPriviledgedHelper(this); } serviceResultString = service.invokeOperation(); if (serviceResultString == null) { errorResponse(response, "Error invoking the operation.<br><b>" + service.getScriptMessage() + "</b>", responseFormat, callbackFunction); freeServiceScript(service); return; } /* Return the results... */ if (serviceResultString != null && serviceResultString.equals("") == false) { writeResponse(serviceResultString, responseFormat, callbackFunction, response); } println(">> Service script executed successfully."); /* Free the service instance... */ freeServiceScript(service); } catch (Exception ex) { errorResponse(response, "Exception processing request: " + ex.toString(), responseFormat, callbackFunction); ex.printStackTrace(); try { freeServiceScript(service); } catch (Exception x) { log.warn("Exception freeing a service instance: " + x.toString()); } return; } println(">> Finished processRequest() at " + new Date()); }
From source file:com.castis.xylophone.adsmadapter.convert.axistree.ConvertMgad.java
@Transactional(rollbackFor = Exception.class, isolation = Isolation.READ_COMMITTED) public int convertAdsInfo(AdsInfo adsInfo, AdsInfo unknownCategoryAdsInfo, String unknownCategoryfileName, String fileName, ADSMSchedulerLogDTO schedulerLog, ADSMSchedulerLogDTO deleteSchedulerLog, InputDataType inputDataType, PlacementOpportunityTypeEnum oppType, PlayInfo playInfo, Platform platformType, InventoryType inventoryType, String subDirectory) throws Exception { int resultCount = 0; long start = System.currentTimeMillis(); log.info("convertAdsInfo start (" + oppType.name() + ", " + inventoryType.name() + ", " + platformType.name() + ")"); this.fileName = fileName; campaignResult = new ResultFileUtil(InputDataType.ADS_INFO); exposurePolicyResult = new ResultFileUtil(InputDataType.EXPOSURE_POLICY); slotNumberPolicyResult = new ResultFileUtil(InputDataType.SLOT_NUMBER_POLICY); try {/* w w w .j a v a2s .c om*/ if (adsInfo != null) { adsInfoResult = new ResultAdsInfo(); adsInfoResult.setXml_ID(adsInfo.getXml_ID()); adsInfoResult.setReg_DT(adsInfo.getReg_DT()); try { timeDefineMap = tambourineConnector.getTimeDefineMap(); if (timeDefineMap != null) timeTreeNodeChildCount = tambourineConnector.getKTTimeTreeNodeChildCountMap(timeDefineMap); } catch (Exception e) { String error = "Time Define load . error : " + e.getMessage(); log.error(error); throw new Exception(error); } if (inputDataType == InputDataType.ADS_INFO) { Date startTime = new Date(start); generateDisablePolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), oppType, playInfo, platformType, inventoryType); /*!*/ generateSlotNumberPolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), inputDataType, oppType, playInfo, platformType, inventoryType); /*!*/ generateGroupRatePolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), oppType, playInfo, platformType, inventoryType); generateContinuosExposurePolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), oppType, playInfo, platformType, inventoryType); generateExposurePolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), inputDataType, oppType, playInfo, platformType, inventoryType); generateADProductPriorityPolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), oppType, playInfo, platformType, inventoryType); //AdCategory_dat generateDisableSameFieldADPolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), oppType, playInfo, platformType, inventoryType); } if (inputDataType == InputDataType.UPDATE_AD_POLICY) { Date startTime = new Date(start); generateSlotNumberPolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), inputDataType, oppType, playInfo, platformType, inventoryType); generateExposurePolicyDTO(adsInfo, startTime, deleteSchedulerLog.getId(), inputDataType, oppType, playInfo, platformType, inventoryType); } if (inputDataType != InputDataType.UPDATE_AD_POLICY) generateADCampaign(adsInfo, unknownCategoryAdsInfo, unknownCategoryfileName, deleteSchedulerLog.getId(), inputDataType, schedulerLog, oppType, playInfo, platformType, inventoryType); schedulerLog.setSchedulerStatus(ADSMSchedulerStatus.SUCCESS); deleteSchedulerLog.setSchedulerStatus(ADSMSchedulerStatus.SUCCESS); //Mgad version DB? ?. if (inputDataType == InputDataType.ADS_INFO) { String version = adsInfo.getAdsVersion(); if (version == null || version.isEmpty()) version = NONE_VERSION; ImportSyncVersion importSyncVersion = new ImportSyncVersion(version, SyncType.ADS_SYNC, schedulerLog.getId()); tambourineConnector.mergeSyncVersion(importSyncVersion); } //update ? ?? ?, ? ? ? ?? ? ?? . if (inputDataType != InputDataType.ADS_INFO) { if (campaignResult.getErrorCount() > 0 || exposurePolicyResult.getErrorCount() > 0 || slotNumberPolicyResult.getErrorCount() > 0) resultCount = -1; } else resultCount = campaignResult.getErrorCount(); } else { adsInfoResult = new ResultAdsInfo(); adsInfoResult.setXml_ID("Parsing error"); adsInfoResult.setReg_DT("Parsing error"); log.error("mgad ?(" + fileName + ") . Data ? ."); schedulerLog.setFailProcess("Parsing error"); schedulerLog.setSchedulerStatus(ADSMSchedulerStatus.FAIL); deleteSchedulerLog.setFailProcess("Parsing error"); deleteSchedulerLog.setSchedulerStatus(ADSMSchedulerStatus.FAIL); campaignResult.setErrorCount(-1); //Parsing error exposurePolicyResult.setErrorCount(-1); //Parsing error slotNumberPolicyResult.setErrorCount(-1); //Parsing error resultCount = -1; } } catch (Exception e) { //log.error("",e); schedulerLog.setMessage(e.getMessage()); schedulerLog.setSchedulerStatus(ADSMSchedulerStatus.FAIL); StackTraceElement[] stackTraces = e.getStackTrace(); if (stackTraces.length > 0) { schedulerLog.setFailProcess(stackTraces[0].getClassName() + " - " + stackTraces[0].getMethodName() + "(" + stackTraces[0].getLineNumber() + ")"); } resultCount = -1; throw e; } finally { ResultFileUtil.writeAdsResultFile(inputDataType, adsInfoResult, exposurePolicyResult, slotNumberPolicyResult, campaignResult, fileName, resultDirectory + subDirectory); } long end = System.currentTimeMillis(); log.info("convertAdsInfo end - T(" + (end - start) + ") (" + oppType.name() + ")"); return resultCount; }
From source file:base.BasePlayer.FileRead.java
static String getVCFLine(String chrom, int start, int end, Sample sample) { if (Draw.variantcalculator) { return ""; }//w w w . jav a 2 s. co m if (sample.calledvariants) { StringBuffer altbases = new StringBuffer(""); int alts = 0, refs = 0; for (int i = 0; i < Main.drawCanvas.varOverLap.vars.size() - 1; i++) { altbases.append(Main.drawCanvas.varOverLap.vars.get(i).getKey()); } alts = Main.drawCanvas.varOverLap.vars.get(0).getValue().get(0).getCalls(); refs = (Main.drawCanvas.varOverLap.vars.get(0).getValue().get(0).getCoverage() - Main.drawCanvas.varOverLap.vars.get(0).getValue().get(0).getCalls()); String genotype = ""; if (alts / (double) refs > 0.95) { genotype = "1/1"; } else { genotype = "0/1"; } altbases.append( Main.drawCanvas.varOverLap.vars.get(Main.drawCanvas.varOverLap.vars.size() - 1).getKey()); return Main.drawCanvas.splits.get(0).chrom + "\t" + (Main.drawCanvas.varOverLap.getPosition() + 1) + "\t.\t" + Main.getBase.get(Main.drawCanvas.varOverLap.getRefBase()) + "\t" + altbases + "\t99\tPASS\tINFO\tGT:AD:DP\t" + genotype + ":" + refs + "," + alts + ":" + (refs + alts); } String line = ""; cancelfileread = false; cancelvarcount = false; try { if (!(VariantHandler.hideIndels.isSelected() && VariantHandler.hideSNVs.isSelected())) { if (sample.multipart) { for (int i = sample.getIndex(); i >= 0; i--) { if (!Main.drawCanvas.sampleList.get(i).multipart) { sample = Main.drawCanvas.sampleList.get(i); break; } } } if (sample.getTabixFile() != null) { setVCFFileStart(chrom, start, end + 3, sample); boolean vcf = sample.getVCFReader() != null; while (line != null) { if (vcf) { try { sample.getVCFReader().ready(); } catch (IOException ex) { } } try { if (vcf) { line = sample.getVCFReader().readLine(); } else { line = sample.getVCFInput().readLine(); } if (line == null || line.split("\t").length < 3 || line.startsWith("#")) { continue; } if (line != null && Integer.parseInt(line.split("\t")[1]) == start + 1) { if (sample.getVCFReader() != null) { sample.getVCFReader().close(); } return line; } } catch (Exception ex) { Main.showError(ex.getMessage(), "Error"); ErrorLog.addError(ex.getStackTrace()); ex.printStackTrace(); Main.cancel(); changing = false; } } if (sample.getVCFReader() != null) { sample.getVCFReader().close(); } return line; } } } catch (Exception exc) { Main.showError(exc.getMessage(), "Error"); System.out.println(sample.getName()); exc.printStackTrace(); ErrorLog.addError(exc.getStackTrace()); changing = false; } return ""; }
From source file:com.asksven.betterbatterystats.StatsActivity.java
@Override protected void onCreate(Bundle savedInstanceState) { SharedPreferences sharedPrefs = PreferenceManager.getDefaultSharedPreferences(this); super.onCreate(savedInstanceState); // HockeyApp/*from w ww . ja v a 2 s . co m*/ try { MetricsManager.register(getApplication()); } catch (Exception e) { Log.e(TAG, e.getMessage()); } //Log.i(TAG, "OnCreated called"); setContentView(R.layout.stats); Toolbar toolbar = (Toolbar) findViewById(R.id.toolbar); toolbar.setTitle(getString(R.string.app_name)); setSupportActionBar(toolbar); getSupportActionBar().setDisplayUseLogoEnabled(false); // set debugging if (sharedPrefs.getBoolean("debug_logging", false)) { LogSettings.DEBUG = true; CommonLogSettings.DEBUG = true; } else { LogSettings.DEBUG = false; CommonLogSettings.DEBUG = false; } swipeLayout = (SwipeRefreshLayout) findViewById(R.id.swiperefresh); swipeLayout.setOnRefreshListener(new SwipeRefreshLayout.OnRefreshListener() { @Override public void onRefresh() { doRefresh(true); } }); /////////////////////////////////////////////// // check if we have a new release /////////////////////////////////////////////// // if yes do some migration (if required) and show release notes String strLastRelease = sharedPrefs.getString("last_release", "0"); String strCurrentRelease = ""; try { PackageInfo pinfo = getPackageManager().getPackageInfo(getPackageName(), 0); strCurrentRelease = Integer.toString(pinfo.versionCode); } catch (Exception e) { // nop strCurrentRelease is set to "" } // Grant permissions if they are missing and root is available if (!SysUtils.hasBatteryStatsPermission(this) || !SysUtils.hasDumpsysPermission(this) || !SysUtils.hasPackageUsageStatsPermission(this)) { if ((RootShell.getInstance().isRooted())) { // attempt to set perms using pm-comand Log.i(TAG, "attempting to grant perms with 'pm grant'"); String pkg = this.getPackageName(); RootShell.getInstance().run("pm grant " + pkg + " android.permission.BATTERY_STATS"); RootShell.getInstance().run("pm grant " + pkg + " android.permission.DUMP"); RootShell.getInstance().run("pm grant " + pkg + " android.permission.PACKAGE_USAGE_STATS"); if (SysUtils.hasBatteryStatsPermission(this)) { Log.i(TAG, "succeeded"); } else { Log.i(TAG, "failed"); } } } // Package usage stats were introduced in SDK21 so we need to make the distinction if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.LOLLIPOP) { // show install as system app screen if root available but perms missing if (!SysUtils.hasBatteryStatsPermission(this) || !SysUtils.hasDumpsysPermission(this) || !SysUtils.hasPackageUsageStatsPermission(this)) { Intent intentSystemApp = new Intent(this, SystemAppActivity.class); this.startActivity(intentSystemApp); } } else { if (!SysUtils.hasBatteryStatsPermission(this) || !SysUtils.hasDumpsysPermission(this)) { Intent intentSystemApp = new Intent(this, SystemAppActivity.class); this.startActivity(intentSystemApp); } } final SharedPreferences prefs = PreferenceManager.getDefaultSharedPreferences(this); // first start if (strLastRelease.equals("0")) { boolean firstLaunch = !prefs.getBoolean("launched", false); if (firstLaunch) { // Save that the app has been launched SharedPreferences.Editor editor = prefs.edit(); editor.putBoolean("launched", true); editor.commit(); // start service to persist reference Intent serviceIntent = new Intent(this, WriteUnpluggedReferenceService.class); this.startService(serviceIntent); // refresh widgets Intent intentRefreshWidgets = new Intent(LargeWidgetProvider.WIDGET_UPDATE); this.sendBroadcast(intentRefreshWidgets); } SharedPreferences.Editor updater = sharedPrefs.edit(); updater.putString("last_release", strCurrentRelease); updater.commit(); } else if (!strLastRelease.equals(strCurrentRelease)) { // save the current release to properties so that the dialog won't be shown till next version SharedPreferences.Editor updater = sharedPrefs.edit(); updater.putString("last_release", strCurrentRelease); updater.commit(); // we don't need to delete refs as long as we don't change the database schema // Toast.makeText(this, getString(R.string.info_deleting_refs), Toast.LENGTH_SHORT).show(); // ReferenceStore.deleteAllRefs(this); // Intent i = new Intent(this, WriteBootReferenceService.class); // this.startService(i); // i = new Intent(this, WriteUnpluggedReferenceService.class); // this.startService(i); ChangeLog cl = new ChangeLog(this); cl.getLogDialog().show(); } /////////////////////////////////////////////// // retrieve default selections for spinners // if none were passed /////////////////////////////////////////////// m_iStat = Integer.valueOf(sharedPrefs.getString("default_stat", "0")); m_refFromName = sharedPrefs.getString("default_stat_type", Reference.UNPLUGGED_REF_FILENAME); if (!ReferenceStore.hasReferenceByName(m_refFromName, this)) { m_refFromName = Reference.BOOT_REF_FILENAME; Toast.makeText(this, getString(R.string.info_fallback_to_boot), Toast.LENGTH_SHORT).show(); } if (LogSettings.DEBUG) Log.i(TAG, "onCreate state from preferences: refFrom=" + m_refFromName + " refTo=" + m_refToName); try { // recover any saved state if ((savedInstanceState != null) && (!savedInstanceState.isEmpty())) { m_iStat = (Integer) savedInstanceState.getSerializable("stat"); m_refFromName = (String) savedInstanceState.getSerializable("stattypeFrom"); m_refToName = (String) savedInstanceState.getSerializable("stattypeTo"); if (LogSettings.DEBUG) Log.i(TAG, "onCreate retrieved saved state: refFrom=" + m_refFromName + " refTo=" + m_refToName); } } catch (Exception e) { m_iStat = Integer.valueOf(sharedPrefs.getString("default_stat", "0")); m_refFromName = sharedPrefs.getString("default_stat_type", Reference.UNPLUGGED_REF_FILENAME); Log.e(TAG, "Exception: " + e.getMessage()); DataStorage.LogToFile(LOGFILE, "Exception in onCreate restoring Bundle"); DataStorage.LogToFile(LOGFILE, e.getMessage()); DataStorage.LogToFile(LOGFILE, e.getStackTrace()); Toast.makeText(this, getString(R.string.info_state_recovery_error), Toast.LENGTH_SHORT).show(); } // Handle the case the Activity was called from an intent with paramaters Bundle extras = getIntent().getExtras(); if ((extras != null) && !extras.isEmpty()) { // Override if some values were passed to the intent if (extras.containsKey(StatsActivity.STAT)) m_iStat = extras.getInt(StatsActivity.STAT); if (extras.containsKey(StatsActivity.STAT_TYPE_FROM)) m_refFromName = extras.getString(StatsActivity.STAT_TYPE_FROM); if (extras.containsKey(StatsActivity.STAT_TYPE_TO)) m_refToName = extras.getString(StatsActivity.STAT_TYPE_TO); if (LogSettings.DEBUG) Log.i(TAG, "onCreate state from extra: refFrom=" + m_refFromName + " refTo=" + m_refToName); boolean bCalledFromNotification = extras.getBoolean(StatsActivity.FROM_NOTIFICATION, false); // Clear the notifications that was clicked to call the activity if (bCalledFromNotification) { NotificationManager nM = (NotificationManager) getSystemService(Service.NOTIFICATION_SERVICE); nM.cancel(EventWatcherService.NOTFICATION_ID); } } // Spinner for selecting the stat Spinner spinnerStat = (Spinner) findViewById(R.id.spinnerStat); ArrayAdapter spinnerStatAdapter = ArrayAdapter.createFromResource(this, R.array.stats, R.layout.bbs_spinner_layout); //android.R.layout.simple_spinner_item); spinnerStatAdapter.setDropDownViewResource(R.layout.bbs_spinner_dropdown_item); // android.R.layout.simple_spinner_dropdown_item); spinnerStat.setAdapter(spinnerStatAdapter); // setSelection MUST be called after setAdapter spinnerStat.setSelection(m_iStat); spinnerStat.setOnItemSelectedListener(this); /////////////////////////////////////////////// // Spinner for Selecting the Stat type /////////////////////////////////////////////// Spinner spinnerStatType = (Spinner) findViewById(R.id.spinnerStatType); m_spinnerFromAdapter = new ReferencesAdapter(this, R.layout.bbs_spinner_layout); //android.R.layout.simple_spinner_item); m_spinnerFromAdapter.setDropDownViewResource(R.layout.bbs_spinner_dropdown_item); //android.R.layout.simple_spinner_dropdown_item); spinnerStatType.setAdapter(m_spinnerFromAdapter); try { this.setListViewAdapter(); } catch (BatteryInfoUnavailableException e) { Log.e(TAG, "Exception: " + Log.getStackTraceString(e)); Snackbar.make(findViewById(android.R.id.content), R.string.info_service_connection_error, Snackbar.LENGTH_LONG).show(); // Toast.makeText(this, // getString(R.string.info_service_connection_error), // Toast.LENGTH_LONG).show(); } catch (Exception e) { //Log.e(TAG, e.getMessage(), e.fillInStackTrace()); Log.e(TAG, "Exception: " + Log.getStackTraceString(e)); Toast.makeText(this, getString(R.string.info_unknown_stat_error), Toast.LENGTH_LONG).show(); } // setSelection MUST be called after setAdapter spinnerStatType.setSelection(m_spinnerFromAdapter.getPosition(m_refFromName)); spinnerStatType.setOnItemSelectedListener(this); /////////////////////////////////////////////// // Spinner for Selecting the end sample /////////////////////////////////////////////// Spinner spinnerStatSampleEnd = (Spinner) findViewById(R.id.spinnerStatSampleEnd); m_spinnerToAdapter = new ReferencesAdapter(this, R.layout.bbs_spinner_layout); //android.R.layout.simple_spinner_item); m_spinnerToAdapter.setDropDownViewResource(R.layout.bbs_spinner_dropdown_item); //android.R.layout.simple_spinner_dropdown_item); spinnerStatSampleEnd.setVisibility(View.VISIBLE); spinnerStatSampleEnd.setAdapter(m_spinnerToAdapter); // setSelection must be called after setAdapter if ((m_refToName != null) && !m_refToName.equals("")) { int pos = m_spinnerToAdapter.getPosition(m_refToName); spinnerStatSampleEnd.setSelection(pos); } else { spinnerStatSampleEnd.setSelection(m_spinnerToAdapter.getPosition(Reference.CURRENT_REF_FILENAME)); } spinnerStatSampleEnd.setOnItemSelectedListener(this); /////////////////////////////////////////////// // sorting /////////////////////////////////////////////// m_iSorting = 0; // log reference store ReferenceStore.logReferences(this); if (LogSettings.DEBUG) { Log.i(TAG, "onCreate final state: refFrom=" + m_refFromName + " refTo=" + m_refToName); Log.i(TAG, "OnCreated end"); } }
From source file:base.BasePlayer.FileRead.java
static void annotate() { if (Main.drawCanvas.splits.get(0).getGenes().size() == 0) { return;//from w w w. j a v a 2s . co m } Transcript transcript; Gene gene, prevGene = Main.drawCanvas.splits.get(0).getGenes().get(0); VarNode current = FileRead.head.getNext(); Transcript.Exon exon; int position = 0, baselength; boolean intronic = true; try { if (current != null) { for (int g = 0; g < Main.drawCanvas.splits.get(0).getGenes().size(); g++) { gene = Main.drawCanvas.splits.get(0).getGenes().get(g); /* while(current != null && current.getPosition() < gene.getStart()) { if(!current.isInGene()) { if(current.getTranscripts() == null) { current.setTranscripts(); } current.getTranscripts().add(prevGene.getTranscripts().get(0)); current.getTranscripts().add(gene.getTranscripts().get(0)); } current = current.getNext(); }*/ if (current == null) { break; } for (int t = 0; t < gene.getTranscripts().size(); t++) { transcript = gene.getTranscripts().get(t); if (current != null && current.getPrev() != null) { while (current.getPrev().getPosition() >= transcript.getStart()) { if (current.getPrev() != null) { current = current.getPrev(); } } } position = current.getPosition(); if (current.indel) { position++; baselength = MethodLibrary.getBaseLength(current.vars, 1); } while (position < transcript.getEnd()) { try { if (position >= transcript.getStart() && position <= transcript.getEnd()) { current.setInGene(); baselength = 0; intronic = true; for (int e = 0; e < transcript.getExons().length; e++) { exon = transcript.getExons()[e]; if (position + baselength >= exon.getStart() - 2 && position < exon.getEnd() + 2) { if (current.getExons() == null) { current.setExons(); } intronic = false; if (!current.getExons().contains(exon)) { current.getExons().add(exon); if (exon.getStartPhase() > -1 && position + baselength >= exon.getTranscript() .getCodingStart() && position < exon.getTranscript().getCodingEnd()) { current.coding = true; } break; } } } if (intronic) { if (current.getTranscripts() == null) { current.setTranscripts(); } current.getTranscripts().add(transcript); } } if (!current.isInGene()) { if (current.getTranscripts() == null) { current.setTranscripts(); current.getTranscripts().add(prevGene.getTranscripts().get(0)); current.getTranscripts().add(gene.getTranscripts().get(0)); } } if (current.getNext() != null) { current = current.getNext(); position = current.getPosition(); } else { break; } } catch (Exception e) { System.out.println(position); e.printStackTrace(); break; } } } if (gene.getEnd() > prevGene.getEnd()) { prevGene = gene; } } while (current != null) { if (!current.isInGene()) { if (current.getTranscripts() == null) { current.setTranscripts(); current.getTranscripts().add(prevGene.getTranscripts().get(0)); current.getTranscripts().add(prevGene.getTranscripts().get(0)); } } current = current.getNext(); } } } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } current = null; transcript = null; exon = null; }
From source file:base.BasePlayer.FileRead.java
void readBED(String url, String index, boolean small) { try {// w ww .j av a 2 s.c o m if (!Main.trackPane.isVisible()) { Main.trackPane.setVisible(true); Main.varpane.setDividerSize(3); Main.varpane.setResizeWeight(0.1); Main.varpane.setDividerLocation(0.1); } else { Main.varpane.setDividerLocation(Main.varpane.getDividerLocation() + 100); Main.varpane.revalidate(); Main.trackPane.setDividerLocation(Main.varpane.getDividerLocation() / 2); if (Main.controlScroll.isVisible()) { Main.trackPane.setDividerSize(3); } } Main.bedScroll.setVisible(true); Main.bedCanvas.setVisible(true); BedTrack addTrack = null; if (index.equals("nan")) { addTrack = new BedTrack(new URL(url), null, Main.bedCanvas.bedTrack.size()); } else { addTrack = new BedTrack(new URL(url), new URL(index), Main.bedCanvas.bedTrack.size()); } //Main.bedCanvas.getBEDfeatures(addTrack, 1, Main.drawCanvas.splits.get(0).chromEnd); if (addTrack != null) { if (url.toLowerCase().endsWith("tsv.gz") || url.toLowerCase().endsWith("tsv.bgz")) { addTrack.getZerobased().setSelected(false); addTrack.iszerobased = 1; addTrack.getSelector().frame.setVisible(true); } addTrack.small = small; Main.bedCanvas.trackDivider.add(0.0); Main.bedCanvas.bedTrack.add(addTrack); setTable(addTrack); if (url.toLowerCase().endsWith(".bedgraph")) { Main.bedCanvas.pressGraph(addTrack); } if (url.toLowerCase().endsWith("bigwig") || url.toLowerCase().endsWith("bw")) { addTrack.small = true; addTrack.bigWig = true; addTrack.graph = true; //Main.bedCanvas.getBEDfeatures(addTrack, (int)Main.drawCanvas.splits.get(0).start, (int)Main.drawCanvas.splits.get(0).end); } setBedTrack(addTrack); if (addTrack.small) { // Main.drawCanvas.loading("loading"); Main.bedCanvas.getBEDfeatures(addTrack, 1, Main.drawCanvas.splits.get(0).chromEnd); //Main.drawCanvas.ready("loading"); } } } catch (Exception e) { e.printStackTrace(); ErrorLog.addError(e.getStackTrace()); } }
From source file:base.BasePlayer.FileRead.java
private void readBAM(File[] files) { try {/*from w ww. j a v a 2s . c o m*/ File addFile = null; File[] addDir; Sample currentSample = null; Boolean added = false; if (files.length == 1 && files[0].getName().endsWith(".link")) { files = readLinkFile(files[0]); } for (int i = 0; i < files.length; i++) { if (files[i].isDirectory()) { addDir = files[i].listFiles(); for (int f = 0; f < addDir.length; f++) { if (addDir[f].getName().endsWith(".bam") || addDir[f].getName().endsWith(".cram")) { addFile = addDir[f]; break; } } } else { if (files[i].getName().endsWith(".bam") || files[i].getName().endsWith(".cram")) { addFile = files[i]; } else { continue; } } if (addFile != null) { Main.drawCanvas.bam = true; currentSample = new Sample(addFile.getName(), (short) Main.samples, null); Main.drawCanvas.sampleList.add(currentSample); currentSample.samFile = addFile; currentSample.resetreadHash(); if (addFile.getName().endsWith(".cram")) { currentSample.CRAM = true; } if (currentSample.samFile.getName().endsWith(".cram")) { currentSample.readString = "CRAM"; } else { currentSample.readString = "BAM"; } try { } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } added = true; Main.readsamples++; Main.samples++; } } if (!added) { return; } checkSamples(); Main.drawCanvas.drawVariables.visiblesamples = (short) (Main.samples); // Main.drawCanvas.checkSampleZoom(); if (Main.drawScroll.getViewport().getHeight() / (Main.drawCanvas.sampleList.size()) > Draw.defaultSampleHeight) { Main.drawCanvas.drawVariables.sampleHeight = Main.drawScroll.getViewport().getHeight() / Main.drawCanvas.sampleList.size(); } else { Main.drawCanvas.drawVariables.sampleHeight = Draw.defaultSampleHeight; } if (Main.drawCanvas.getHeight() < (Main.drawCanvas.sampleList.size()) * Main.drawCanvas.drawVariables.sampleHeight) { Main.drawCanvas.resizeCanvas(Main.drawCanvas.getWidth(), (int) ((Main.drawCanvas.sampleList.size()) * Main.drawCanvas.drawVariables.sampleHeight)); Main.drawCanvas.revalidate(); } } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } Draw.updateReads = true; Draw.updatevars = true; Main.drawCanvas.repaint(); }