Java tutorial
/************************************************************************** Copyright (c) 2011: Istituto Nazionale di Fisica Nucleare (INFN), Italy Consorzio COMETA (COMETA), Italy See http://www.infn.it and and http://www.consorzio-cometa.it for details on the copyright holders. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. @author <a href="mailto:diego-rincon@javeriana.edu.co">Diego Alberto Rincn Yez</a>(JAVERIANA) @author <a href="mailto:dburbano@uniandes.edu.co">Daniel Alberto Burbano Sefair</a>(UNIANDES) @author <a href="mailto:riccardo.rotondo@garr.it">Riccardo Rotondo</a>(GARR) @author <a href="mailto:giuseppe.larocca@ct.infn.it">Giuseppe La Rocca</a>(INFN ) ****************************************************************************/ package it.infn.ct; // Import generic java libraries import java.io.*; import java.net.*; import java.util.Iterator; import java.util.List; import java.util.Calendar; import java.text.SimpleDateFormat; // Importing portlet libraries import javax.portlet.*; // Importing liferay libraries import com.liferay.portal.util.PortalUtil; import com.liferay.portal.kernel.util.WebKeys; import com.liferay.portal.kernel.exception.PortalException; import com.liferay.portal.kernel.exception.SystemException; import com.liferay.portal.theme.ThemeDisplay; import com.liferay.portal.model.Company; import com.liferay.portal.model.User; // Importing Apache libraries import org.apache.commons.fileupload.*; import org.apache.commons.fileupload.disk.DiskFileItemFactory; import org.apache.commons.fileupload.portlet.PortletFileUpload; // Importing GridEngine Job libraries import it.infn.ct.GridEngine.Job.*; import it.infn.ct.GridEngine.Job.MultiInfrastructureJobSubmission; import it.infn.ct.GridEngine.UsersTracking.UsersTrackingDBInterface; // Logging import java.util.logging.Level; import java.util.logging.Logger; /** * This is the class that overrides the GenericPortlet class methods * You can create your own application just customizing this code skeleton * This code provides mainly a full working example on: * 1) How to manage user interaction managing the Actions/Viewa combination * 2) How to manage portlet preferences and help pane * 3) How to print application information using the Log object * 4) How to execute a distributed application with GridEngine * * @author <a href="mailto:riccardo.bruno@ct.infn.it">Riccardo Bruno</a>(COMETA) */ public class g_hmmer_portlet extends GenericPortlet { // Instantiate the logger object AppLogger _log = new AppLogger(g_hmmer_portlet.class); // This portlet uses Aciont/Views enumerations in order to // manage the different portlet modes and the corresponding // view to display // You may override the current values with your own business // logic best identifiers and manage them through: jsp pages and // this java code // The jsp parameter PortletStatus will be the responsible of // portlet mode switching. This parameter will be read by // the processAction method (actionRequest) who will select // then the proper view mode. The doView method will read this // value (renderResponSe) assigning the correct view mode. // // At first boot the application will be in ACTIVATE status // that means the application still requires to be registered // into the GridEngine' UsersTrackingDB' GridOperations table // Once registered the defaul view mode will be the VIEW_INPUT /** * Actions enumeration contains the possible action status mode * managed by the application. Action modes are stored into the 'PortletStatus' * parameter inside the actionRequest object */ private enum Actions { ACTION_ACTIVATE // User (Admin) activated the portlet , ACTION_INPUT // User asked to submit a job , ACTION_SUBMIT // User asked to rerutn to the input form , ACTION_PILOT // The user did something in the edit pilot screen pane } /** * Views enumeration contains the possible view mondes managed b * the application. View modes are stored into the parameter 'PortletStatus' * inside the renderResponse object */ private enum Views { VIEW_ACTIVATE // Show acrivation pane (called 1st time only) , VIEW_INPUT // View containing application input fields , VIEW_SUBMIT // View reporting the job submission , VIEW_PILOT // Shows the pilot script and makes it editable } /** * Instanciate the AppPreferences object that stores the Application preferences * * @see AppPreferences */ AppPreferences appPreferences = new AppPreferences(_log); AppPreferences appInitPreferences = new AppPreferences(_log); /** * This class contains all the necessary data to submit a job inside * a distributed infrastructure. Each submission will instanciate this * object */ class AppInput { // Applicatoin inputs String inputFileName; // Filename for application input file String inputFileText; // Text for application input file String jobIdentifier; // User' given job identifier // Each inputSandobox file must be declared below // This variable contains the content of an uploaded file String inputSandbox_inputFile; // Some user level information // must be stored as well String username; String timestamp; /** * Standard constructor just initialize empty values */ public AppInput() { inputFileName = inputFileText = jobIdentifier = inputSandbox_inputFile = username = timestamp = ""; } } // AppInput // Liferay portal data // Classes below are used by this portlet code to get information // about the current user public String portalName = "localhost"; // Name of the hosting portal public String appServerPath; // This variable stores the absolute path of the Web applications // Other misc valuse // (!) Pay attention that altough the use of the LS variable // the replaceAll("\n","") has to be used public static final String LS = System.getProperty("line.separator"); // Users must have separated inputSandbox files // these file will be generated into /tmp directory // and prefixed with the format <timestamp>_<user>_* // The timestamp format is: public static final String tsFormat = "yyyyMMddHHmmss"; // This variable holds the GridEngine' GridOperation identifier // associated to this application int gridOperationId = -1; //---------------------------- // Portlet Overriding Methods //---------------------------- /** * The init method will be called when installing the portlet for the first time * or when restarting the portal server. * This is the right time to get default values from WEBINF/portlet.xml file * Those values will be assigned into the application preferences as default values * If preference values already exists for this application the default settings will * be overwritten * * @see AppInfrastructureInfo * @see AppPreferences * * @throws PortletException */ @Override public void init() throws PortletException { // Load default values from WEBINF/portlet.xml appInitPreferences.setGridOperationDesc("" + getInitParameter("gridOperationDesc")); appInitPreferences.setPortletVersion("" + getInitParameter("portletVersion")); appInitPreferences.setLogLevel("" + getInitParameter("logLevel")); appInitPreferences.setNumInfrastructures("" + getInitParameter("numInfrastructures")); appInitPreferences.setGridOperationId("" + getInitParameter("gridOperationId")); // Get the number of infrastructures to load int numInfra = appInitPreferences.getNumInfrastructures(); _log.info("Number of infrastructures: '" + numInfra + "'"); // Load infrastructure settings for (int i = 0; i < numInfra; i++) { int j = i + 1; appInitPreferences.setInfrastructure(i, "" + getInitParameter(j + "_enableInfrastructure"), "" + getInitParameter(j + "_nameInfrastructure"), "" + getInitParameter(j + "_acronymInfrastructure"), "" + getInitParameter(j + "_bdiiHost"), "" + getInitParameter(j + "_wmsHosts"), "" + getInitParameter(j + "_pxServerHost"), "" + getInitParameter(j + "_pxServerPort"), "" + getInitParameter(j + "_pxServerSecure"), "" + getInitParameter(j + "_pxRobotId"), "" + getInitParameter(j + "_pxRobotVO"), "" + getInitParameter(j + "_pxRobotRole"), "" + getInitParameter(j + "_pxRobotRenewalFlag"), "" + getInitParameter(j + "_pxUserProxy"), "" + getInitParameter(j + "_softwareTags")); } // Load infrastructure settings appInitPreferences.setSciGwyUserTrackingDB_Hostname("" + getInitParameter("sciGwyUserTrackingDB_Hostname")); appInitPreferences.setSciGwyUserTrackingDB_Username("" + getInitParameter("sciGwyUserTrackingDB_Username")); appInitPreferences.setSciGwyUserTrackingDB_Password("" + getInitParameter("sciGwyUserTrackingDB_Password")); appInitPreferences.setSciGwyUserTrackingDB_Database("" + getInitParameter("sciGwyUserTrackingDB_Database")); appInitPreferences.setJobRequirements("" + getInitParameter("jobRequirements")); appInitPreferences.setPilotScript("" + getInitParameter("pilotScript")); // Assigns the log level _log.setLogLevel(appInitPreferences.getLogLevel()); // Show loaded values into log _log.debug(appInitPreferences.dump()); } // init /** * This method allows the portlet to process an action request; this method is normally * called upon each user interaction (i.e. A submit button inside a jsp' <form statement) * This method determines the current application mode through the actionRequest value: * 'PortletStatus' and then determines the correct view mode to assign through the * ActionResponse 'PortletStatus' variable that will be read by the doView * This method will also takes care about the std JSR168/286: EDIT and HELP portlet modes. * * @param request ActionRequest object instance * @param response ActionResponse object instance * * @throws PortletException * @throws IOException */ @Override public void processAction(ActionRequest request, ActionResponse response) throws PortletException, IOException { _log.info("calling processAction ..."); // Determine the username ThemeDisplay themeDisplay = (ThemeDisplay) request.getAttribute(WebKeys.THEME_DISPLAY); User user = themeDisplay.getUser(); String username = user.getScreenName(); // Determine the application pathname PortletSession portletSession = request.getPortletSession(); PortletContext portletContext = portletSession.getPortletContext(); appServerPath = portletContext.getRealPath("/"); // Show info _log.info("appUserName : '" + username + "'" + LS + "appServerPath : '" + appServerPath + "'"); // Determine the current portlet mode and forward this state to the response // Accordingly to JSRs168/286 the standard portlet modes are: // VIEW, EDIT, HELP PortletMode mode = request.getPortletMode(); response.setPortletMode(mode); // Switch among different portlet modes: VIEW, EDIT, HELP // any custom modes are not covered by this template //---------- // VIEW Mode // // The actionStatus value will be taken from the calling jsp file // through the 'PortletStatus' parameter; the corresponding // VIEW mode will be stored registering the portlet status // as render parameter. See the call to setRenderParameter // If the actionStatus parameter is null or empty the default // action will be the ACTION_INPUT (input form) // This happens the first time the portlet is shown // The PortletStatus variable is managed by jsp and this java code //---------- if (mode.equals(PortletMode.VIEW)) { // The VIEW mode is the normal portlet mode where normal portlet // content will be shown to the user _log.info("Portlet mode: VIEW"); String actionStatus = request.getParameter("PortletStatus"); // Assigns the default ACTION mode if (null == actionStatus || actionStatus.equals("")) actionStatus = "" + Actions.ACTION_INPUT; // Different actions will be performed accordingly to the // different possible statuses switch (Actions.valueOf(actionStatus)) { case ACTION_ACTIVATE: _log.info("Got action: 'ACTION_ACTIVATE'"); // Called when activating the portlet for the first time // it will be used to save the gridOperationId value // into the application preferences gridOperationId = Integer.parseInt(request.getParameter("gridOperationId")); _log.info("Received gridOperationId: '" + gridOperationId + "'"); // If the application is registered go to the VIEW_INPUT // and the application will no longer go to the ACTIVATE pane if (gridOperationId > 0) { storePreferences(request); response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT); } break; case ACTION_INPUT: _log.info("Got action: 'ACTION_INPUT'"); // Assign the correct view response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT); break; case ACTION_PILOT: _log.info("Got action: 'ACTION_PILOT'"); // Stores the new pilot script String pilotScript = request.getParameter("pilotScript"); pilotScript.replaceAll("\r", ""); storeString(appServerPath + "WEB-INF/job/" + appPreferences.getPilotScript(), pilotScript); // Assign the correct view response.setPortletMode(PortletMode.EDIT); break; case ACTION_SUBMIT: _log.info("Got action: 'ACTION_SUBMIT'"); // Get current preference values getPreferences(request, null); // Create the appInput object AppInput appInput = new AppInput(); // Stores the user submitting the job appInput.username = username; // Determine the submissionTimeStamp SimpleDateFormat dateFormat = new SimpleDateFormat(tsFormat); String timestamp = dateFormat.format(Calendar.getInstance().getTime()); appInput.timestamp = timestamp; // Process input fields and files to upload getInputForm(request, appInput); // Following files have to be updated with // values taken from textareas or from uploaded files: // input_file.txt updateFiles(appInput); // Submit the job submitJob(appInput); // Send the jobIdentifier and assign the correct view response.setRenderParameter("PortletStatus", "" + Views.VIEW_SUBMIT); response.setRenderParameter("jobIdentifier", "" + appInput.jobIdentifier); break; default: _log.info("Unhandled action: '" + actionStatus + "'"); response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT); } // switch actionStatus } // VIEW //---------- // HELP Mode // // The HELP mode used to give portlet usage HELP to the user // This code will be called after the call to doHelp method //---------- else if (mode.equals(PortletMode.HELP)) { _log.info("Portlet mode: HELP"); } //---------- // EDIT Mode // // The EDIT mode is used to view/setup portlet preferences // This code will be called after the user sends the actionURL // generated by the doEdit method // The code below just stores new preference values or // reacts to the preference settings changes //---------- else if (mode.equals(PortletMode.EDIT)) { _log.info("Portlet mode: EDIT"); // Retrieve the current ifnrstructure in preference int numInfrastructures = appPreferences.getNumInfrastructures(); int currInfra = appPreferences.getCurrPaneInfrastructure(); _log.info(LS + "Number of infrastructures: '" + numInfrastructures + "'" + LS + "currentInfrastructure: '" + currInfra + "'" + LS); // Take care of the preference action (Infrastructure preferences) // <,>,+,- buttons String pref_action = "" + request.getParameter("pref_action"); _log.info("pref_action: '" + pref_action + "'"); // Reacts to the current infrastructure change and // determine the next view mode (return to the input pane) if (pref_action.equalsIgnoreCase("next")) { appPreferences.switchNextInfrastructure(); _log.info("Got next infrastructure action; switching to: '" + appPreferences.getCurrPaneInfrastructure() + "'"); } else if (pref_action.equalsIgnoreCase("previous")) { appPreferences.switchPreviousInfrastructure(); _log.info("Got prev infrastructure action; switching to: '" + appPreferences.getCurrPaneInfrastructure() + "'"); } else if (pref_action.equalsIgnoreCase("add")) { appPreferences.addNewInfrastructure(); _log.info("Got add infrastructure action; current infrastrucure is now: '" + appPreferences.getCurrPaneInfrastructure() + "'"); } else if (pref_action.equalsIgnoreCase("remove")) { appPreferences.delCurrInfrastructure(); _log.info("Got remove infrastructure action; current infrastrucure is now: '" + appPreferences.getCurrPaneInfrastructure() + "' and infrastructures are now: '" + appPreferences.getNumInfrastructures() + "'"); } else if (pref_action.equalsIgnoreCase("done")) { // None of the above actions selected; return to the VIEW mode response.setPortletMode(PortletMode.VIEW); response.setRenderParameter("PortletStatus", "" + Views.VIEW_INPUT); } else if (pref_action.equalsIgnoreCase("viewPilot")) { // None of the above actions selected; return to the VIEW mode response.setPortletMode(PortletMode.VIEW); response.setRenderParameter("PortletStatus", "" + Views.VIEW_PILOT); response.setRenderParameter("pilotScript", updateString(appServerPath + "WEB-INF/job/" + appPreferences.getPilotScript())); } else { // No other special actions to do ... } // Number of infrastructures and Currentinfrastructure values // may be changed by add/delete,<,> actions int newCurrInfra = appPreferences.getCurrPaneInfrastructure(); int newNumInfrastructures = appPreferences.getNumInfrastructures(); // Store infrastructure changes String infrastructuresInformations = ""; // Preference settings (logLevel has been taken above) String newpref_logLevel = "" + request.getParameter("pref_logLevel"); String newpref_gridOperationId = "" + request.getParameter("pref_gridOperationId"); String newpref_jobRequirements = "" + request.getParameter("pref_jobRequirements"); String newpref_pilotScript = "" + request.getParameter("pref_pilotScript"); // Store infrastructure changes only if the user did not select the delete button if (newNumInfrastructures >= numInfrastructures) { // Current infrastructure preference settings AppInfrastructureInfo newpref_appInfrastructureInfo = new AppInfrastructureInfo( "" + request.getParameter("pref_enableInfrastructure"), "" + request.getParameter("pref_nameInfrastructure"), "" + request.getParameter("pref_acronymInfrastructure"), "" + request.getParameter("pref_bdiiHost"), "" + request.getParameter("pref_wmsHosts"), "" + request.getParameter("pref_pxServerHost"), "" + request.getParameter("pref_pxServerPort"), "" + request.getParameter("pref_pxServerSecure"), "" + request.getParameter("pref_pxRobotId"), "" + request.getParameter("pref_pxRobotVO"), "" + request.getParameter("pref_pxRobotRole"), "" + request.getParameter("pref_pxRobotRenewalFlag"), "" + request.getParameter("pref_pxUserProxy"), "" + request.getParameter("pref_softwareTags")); // newNumInfrastructures == numInfrastructures // the user selected < or > buttons; changes goes to the old (currInfra) value // otherwise + has been selected; changes goes again on the old (currInfra) value // the - case has been filtered out by newNumInfrastructures >= numInfrastructures String pref_enableInfrastructure = appPreferences.getEnableInfrastructure(currInfra - 1); String pref_nameInfrastructure = appPreferences.getNameInfrastructure(currInfra - 1); String pref_acronymInfrastructure = appPreferences.getAcronymInfrastructure(currInfra - 1); String pref_bdiiHost = appPreferences.getBdiiHost(currInfra - 1); String pref_wmsHosts = appPreferences.getWmsHosts(currInfra - 1); String pref_pxServerHost = appPreferences.getPxServerHost(currInfra - 1); String pref_pxServerPort = appPreferences.getPxServerPort(currInfra - 1); String pref_pxServerSecure = appPreferences.getPxServerSecure(currInfra - 1); String pref_pxRobotId = appPreferences.getPxRobotId(currInfra - 1); String pref_pxRobotVO = appPreferences.getPxRobotVO(currInfra - 1); String pref_pxRobotRole = appPreferences.getPxRobotRole(currInfra - 1); String pref_pxRobotRenewalFlag = appPreferences.getPxRobotRenewalFlag(currInfra - 1); String pref_pxUserProxy = appPreferences.getPxUserProxy(currInfra - 1); String pref_softwareTags = appPreferences.getSoftwareTags(currInfra - 1); // New preference values String newpref_enableInfrastructure = newpref_appInfrastructureInfo.getEnableInfrastructure(); String newpref_nameInfrastructure = newpref_appInfrastructureInfo.getNameInfrastructure(); String newpref_acronymInfrastructure = newpref_appInfrastructureInfo.getAcronymInfrastructure(); String newpref_bdiiHost = newpref_appInfrastructureInfo.getBdiiHost(); String newpref_wmsHosts = newpref_appInfrastructureInfo.getWmsHosts(); String newpref_pxServerHost = newpref_appInfrastructureInfo.getPxServerHost(); String newpref_pxServerPort = newpref_appInfrastructureInfo.getPxServerPort(); String newpref_pxServerSecure = newpref_appInfrastructureInfo.getPxServerSecure(); String newpref_pxRobotId = newpref_appInfrastructureInfo.getPxRobotId(); String newpref_pxRobotVO = newpref_appInfrastructureInfo.getPxRobotVO(); String newpref_pxRobotRole = newpref_appInfrastructureInfo.getPxRobotRole(); String newpref_pxRobotRenewalFlag = newpref_appInfrastructureInfo.getPxRobotRenewalFlag(); String newpref_pxUserProxy = newpref_appInfrastructureInfo.getPxUserProxy(); String newpref_softwareTags = newpref_appInfrastructureInfo.getSoftwareTags(); // Prepare the Log string with differences infrastructuresInformations += LS + "Infrastructure #" + currInfra + LS + " enableInfrastructure : '" + pref_enableInfrastructure + "' -> '" + newpref_enableInfrastructure + "'" + LS + " nameInfrastructures : '" + pref_nameInfrastructure + "' -> '" + newpref_nameInfrastructure + "'" + LS + " acronymInfrastructures: '" + pref_acronymInfrastructure + "' -> '" + newpref_acronymInfrastructure + "'" + LS + " bdiiHost : '" + pref_bdiiHost + "' -> '" + newpref_bdiiHost + "'" + LS + " wmsHosts : '" + pref_wmsHosts + "' -> '" + newpref_wmsHosts + "'" + LS + " pxServerHost : '" + pref_pxServerHost + "' -> '" + newpref_pxServerHost + "'" + LS + " pxServerPort : '" + pref_pxServerPort + "' -> '" + newpref_pxServerPort + "'" + LS + " pxServerSecure : '" + pref_pxServerSecure + "' -> '" + newpref_pxServerSecure + "'" + LS + " pxRobotId : '" + pref_pxRobotId + "' -> '" + newpref_pxRobotId + "'" + LS + " pxRobotVO : '" + pref_pxRobotVO + "' -> '" + newpref_pxRobotVO + "'" + LS + " pxRobotRole : '" + pref_pxRobotRole + "' -> '" + newpref_pxRobotRole + "'" + LS + " pxRobotRenewalFlag : '" + pref_pxRobotRenewalFlag + "' -> '" + newpref_pxRobotRenewalFlag + "'" + LS + " pxUserProxy : '" + pref_pxUserProxy + "' -> '" + newpref_pxUserProxy + "'" + LS + " softwareTags : '" + pref_softwareTags + "' -> '" + newpref_softwareTags + "'" + LS; // Assigns the new values appPreferences.setInfrastructure(currInfra - 1, newpref_enableInfrastructure, newpref_nameInfrastructure, newpref_acronymInfrastructure, newpref_bdiiHost, newpref_wmsHosts, newpref_pxServerHost, newpref_pxServerPort, newpref_pxServerSecure, newpref_pxRobotId, newpref_pxRobotVO, newpref_pxRobotRole, newpref_pxRobotRenewalFlag, newpref_pxUserProxy, newpref_softwareTags); } // newCurrInfra >= currInfra // Show preference value changes _log.info(LS + "variable name : 'Old Value' -> 'New value'" + LS + "---------------------------------------------------" + LS + "pref_logLevel : '" + appPreferences.getLogLevel() + "' -> '" + newpref_logLevel + "'" + LS + "pref_gridOperationId : '" + appPreferences.getGridOperationId() + "' -> '" + newpref_gridOperationId + "'" + LS + "pref_numInfrastructures: '" + appPreferences.getNumInfrastructures() + "' -> '" + numInfrastructures + "'"); _log.debug(LS + infrastructuresInformations); _log.info(LS + "pref_jobRequirements : '" + appPreferences.getJobRequirements() + "' -> '" + newpref_jobRequirements + "'" + LS + "pref_pilotScript : '" + appPreferences.getPilotScript() + "' -> '" + newpref_pilotScript + "'"); // Assign the new variable to the preference object appPreferences.setLogLevel(newpref_logLevel); appPreferences.setGridOperationId(newpref_gridOperationId); appPreferences.setJobRequirements(newpref_jobRequirements); appPreferences.setPilotScript(newpref_pilotScript); // Store new preferences storePreferences(request); } // EDIT Mode //---------- // EDIT Mode // // Any custom portlet mode should be placed here below //---------- else { // Unsupported portlet modes come here _log.warn("Custom portlet mode: '" + mode.toString() + "'"); } // CUSTOM Mode } // processAction /** * This method is responsible to assign the correct Application view * the view mode is taken from the renderRequest instance by the PortletStatus patameter * or automatically assigned accordingly to the Application status/default view mode * * @param request RenderRequest instance normally sent by the processAction * @param response RenderResponse used to send values to the jsp page * * @throws PortletException * @throws IOException */ @Override protected void doView(RenderRequest request, RenderResponse response) throws PortletException, IOException { _log.info("calling doView ..."); response.setContentType("text/html"); // Get current preference values getPreferences(null, request); gridOperationId = Integer.parseInt(appPreferences.getGridOperationId()); _log.info("GridOperationId: '" + gridOperationId + "'"); // currentView comes from the processAction; unless such method // is not called before (example: page shown with no user action) // In case the application is not yet register (gridOperationId<0) // the VIEW_INITIALIZE pane will be enforced otherwise the // VIEW_INPUT will be selected as default view String currentView = request.getParameter("PortletStatus"); if (currentView == null) currentView = "VIEW_INPUT"; if (gridOperationId < 0) currentView = "VIEW_ACTIVATE"; // Different actions will be performed accordingly to the // different possible view modes switch (Views.valueOf(currentView)) { // The following code is responsible to call the proper jsp file // that will provide the correct portlet interface case VIEW_ACTIVATE: { _log.info("VIEW_ACTIVATE Selected ..."); } break; case VIEW_INPUT: { _log.info("VIEW_INPUT Selected ..."); PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/input.jsp"); dispatcher.include(request, response); } break; case VIEW_PILOT: { _log.info("VIEW_PILOT Selected ..."); String pilotScript = request.getParameter("pilotScript"); request.setAttribute("pilotScript", pilotScript); PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/viewPilot.jsp"); dispatcher.include(request, response); } break; case VIEW_SUBMIT: { _log.info("VIEW_SUBMIT Selected ..."); String jobIdentifier = request.getParameter("jobIdentifier"); request.setAttribute("jobIdentifier", jobIdentifier); PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/submit.jsp"); dispatcher.include(request, response); } break; default: _log.info("Unknown view mode: " + currentView.toString()); } // switch } // doView /** * This method is responsible to retrieve the current Application preference settings * and then show the edit.jsp page where the user can edit the Application preferences * This methods prepares an actionURL that will be used by edit.jsp file into a <input ...> form * As soon the user press the action button the processAction will be called going in EDIT mode * This method is equivalent to the doView method * * @param request Render request object instance * @param response Render response object isntance * * @throws PortletException * @throws IOException * */ @Override public void doEdit(RenderRequest request, RenderResponse response) throws PortletException, IOException { response.setContentType("text/html"); _log.info("Calling doEdit ..."); // Get current preference values getPreferences(null, request); // Get the current infrastructure and the number of infrastructure int currInfra = appPreferences.getCurrPaneInfrastructure(); int numInfrastructures = appPreferences.getNumInfrastructures(); // ActionURL and the current preference value will be passed to the edit.jsp PortletURL pref_actionURL = response.createActionURL(); request.setAttribute("pref_actionURL", pref_actionURL.toString()); // Send preference values request.setAttribute("pref_logLevel", "" + appPreferences.getLogLevel()); request.setAttribute("pref_numInfrastructures", "" + appPreferences.getNumInfrastructures()); request.setAttribute("pref_currInfrastructure", "" + appPreferences.getCurrPaneInfrastructure()); request.setAttribute("pref_gridOperationId", "" + appPreferences.getGridOperationId()); request.setAttribute("pref_gridOperationDesc", "" + appPreferences.getGridOperationDesc()); // Send Infrastructure specific data if (0 <= currInfra && currInfra <= numInfrastructures) { request.setAttribute("pref_enableInfrastructure", appPreferences.getEnableInfrastructure(currInfra - 1)); request.setAttribute("pref_nameInfrastructure", appPreferences.getNameInfrastructure(currInfra - 1)); request.setAttribute("pref_acronymInfrastructure", appPreferences.getAcronymInfrastructure(currInfra - 1)); request.setAttribute("pref_bdiiHost", appPreferences.getBdiiHost(currInfra - 1)); request.setAttribute("pref_wmsHosts", appPreferences.getWmsHosts(currInfra - 1)); request.setAttribute("pref_pxServerHost", appPreferences.getPxServerHost(currInfra - 1)); request.setAttribute("pref_pxServerPort", appPreferences.getPxServerPort(currInfra - 1)); request.setAttribute("pref_pxServerSecure", appPreferences.getPxServerSecure(currInfra - 1)); request.setAttribute("pref_pxRobotId", appPreferences.getPxRobotId(currInfra - 1)); request.setAttribute("pref_pxRobotVO", appPreferences.getPxRobotVO(currInfra - 1)); request.setAttribute("pref_pxRobotRole", appPreferences.getPxRobotRole(currInfra - 1)); request.setAttribute("pref_pxRobotRenewalFlag", appPreferences.getPxRobotRenewalFlag(currInfra - 1)); request.setAttribute("pref_pxUserProxy", appPreferences.getPxUserProxy(currInfra - 1)); request.setAttribute("pref_softwareTags", appPreferences.getSoftwareTags(currInfra - 1)); } // if paneInfrastructure > 0 request.setAttribute("pref_jobRequirements", appPreferences.getJobRequirements()); request.setAttribute("pref_pilotScript", appPreferences.getPilotScript()); // The edit.jsp will be the responsible to show/edit the current preference values PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/edit.jsp"); dispatcher.include(request, response); } // doEdit /** * This method just calls the jsp responsible to show the portlet information * This method is equivalent to the doView method * * @param request Render request object instance * @param response Render response object isntance * * @throws PortletException * @throws IOException */ @Override public void doHelp(RenderRequest request, RenderResponse response) throws PortletException, IOException { _log.info("Calling doHelp ..."); response.setContentType("text/html"); request.setAttribute("portletVersion", appPreferences.getPortletVersion()); PortletRequestDispatcher dispatcher = getPortletContext().getRequestDispatcher("/help.jsp"); dispatcher.include(request, response); } // doHelp //---------------------------- // Portlet Standard Methods //---------------------------- /** * This method is used to retrieve from the Application preferences the * GridEngine' GridOperations identifier associated to this application * Such index is automatically created when registering the application * with the couple (portalName,applicationDesc) * The portal name is automatically extracted from the Application * The portal description is defined in the default parameters (portlet.xml) * This method can be called by processAction or doViewe evakuating one of the * corresponding actionRequest or renderRequest object instances * * @param actionRequest an ActionRequest instance or, * @param renderRequest a RenderRequest instance * @return The GridOperationId associated to this application or -1 if the application is not yet registered * * @see AppPreferences * private String getPrefGridOperationId(ActionRequest actionRequest , RenderRequest renderRequest) { PortletPreferences portletPreferences; String prefOperationId=""; if(null != actionRequest) { portletPreferences= actionRequest.getPreferences(); prefOperationId = portletPreferences.getValue("pref_gridOperationId","-1"); } if(null != renderRequest) { portletPreferences= renderRequest.getPreferences(); prefOperationId = portletPreferences.getValue("pref_gridOperationId","-1"); } return prefOperationId; } */ /** * This method Uses the AppPreference object settings to store Application preferences * * @param request ActinRequest instance (called by the processAction) * * @throws PortletException * @throws IOException */ void storePreferences(ActionRequest request) throws PortletException, IOException { _log.info("Calling storePreferences ..."); // Stored preference content String storedPrefs = "Stored preferences:" + LS + "-------------------" + LS; // The code below stores all the portlet preference values PortletPreferences prefs = request.getPreferences(); if (prefs != null) { String logLevel = appPreferences.getLogLevel(); String gridOperationId = appPreferences.getGridOperationId(); int numInfrastructures = appPreferences.getNumInfrastructures(); int currPaneInfrastructure = appPreferences.getCurrPaneInfrastructure(); String gridOperationDesc = appPreferences.getGridOperationDesc(); prefs.setValue("pref_logLevel", "" + logLevel); prefs.setValue("pref_gridOperationId", "" + gridOperationId); prefs.setValue("pref_gridOperationDesc", "" + gridOperationDesc); prefs.setValue("pref_numInfrastructures", "" + numInfrastructures); prefs.setValue("pref_currInfrastructure", "" + currPaneInfrastructure); storedPrefs += "pref_logLevel : '" + logLevel + "'" + LS + "pref_gridOperationId : '" + gridOperationId + "'" + LS + "pref_gridOperationDesc : '" + gridOperationDesc + "'" + LS + "pref_numInfrastructures : '" + numInfrastructures + "'" + LS + "pref_currInfrastructure : '" + currPaneInfrastructure + "'" + LS; // For each preference infrastructure for (int i = 0; i < numInfrastructures; i++) { int j = i + 1; storedPrefs = LS + "Infrastructure #" + j + LS + "--------------------" + LS; String enableInfrastructure = appPreferences.getEnableInfrastructure(i); String nameInfrastructure = appPreferences.getNameInfrastructure(i); String acronymInfrastructure = appPreferences.getAcronymInfrastructure(i); String bdiiHost = appPreferences.getBdiiHost(i); String wmsHost = appPreferences.getWmsHosts(i); String pxServerHost = appPreferences.getPxServerHost(i); String pxServerPort = appPreferences.getPxServerPort(i); String pxServerSecure = appPreferences.getPxServerSecure(i); String pxRobotId = appPreferences.getPxRobotId(i); String pxRobotVO = appPreferences.getPxRobotVO(i); String pxRobotRole = appPreferences.getPxRobotRole(i); String pxRobotRenewalFlag = appPreferences.getPxRobotRenewalFlag(i); String pxUserProxy = appPreferences.getPxUserProxy(i); String softwareTags = appPreferences.getSoftwareTags(i); // Set preference values prefs.setValue("pref_" + j + "_enableInfrastructure", enableInfrastructure); prefs.setValue("pref_" + j + "_nameInfrastructure", nameInfrastructure); prefs.setValue("pref_" + j + "_acronymInfrastructure", acronymInfrastructure); prefs.setValue("pref_" + j + "_bdiiHost", bdiiHost); prefs.setValue("pref_" + j + "_wmsHosts", wmsHost); prefs.setValue("pref_" + j + "_pxServerHost", pxServerHost); prefs.setValue("pref_" + j + "_pxServerPort", pxServerPort); prefs.setValue("pref_" + j + "_pxServerSecure", pxServerSecure); prefs.setValue("pref_" + j + "_pxRobotId", pxRobotId); prefs.setValue("pref_" + j + "_pxRobotVO", pxRobotVO); prefs.setValue("pref_" + j + "_pxRobotRole", pxRobotRole); prefs.setValue("pref_" + j + "_pxRobotRenewalFlag", pxRobotRenewalFlag); prefs.setValue("pref_" + j + "_pxUserProxy", pxUserProxy); prefs.setValue("pref_" + j + "_softwareTags", softwareTags); // Dumps the infrastructure preferences storedPrefs += " pref_" + j + "_enableInfrastructure : '" + enableInfrastructure + "'" + LS + " pref_" + j + "_nameInfrastructure : '" + nameInfrastructure + "'" + LS + " pref_" + j + "_acronymInfrastructure: '" + acronymInfrastructure + "'" + LS + " pref_" + j + "_bdiiHost : '" + bdiiHost + "'" + LS + " pref_" + j + "_wmsHosts : '" + wmsHost + "'" + LS + " pref_" + j + "_pxServerHost : '" + pxServerHost + "'" + LS + " pref_" + j + "_pxServerPort : '" + pxServerPort + "'" + LS + " pref_" + j + "_pxServerSecure : '" + pxServerSecure + "'" + LS + " pref_" + j + "_pxRobotId : '" + pxRobotId + "'" + LS + " pref_" + j + "_pxRobotVO : '" + pxRobotVO + "'" + LS + " pref_" + j + "_pxRobotRole : '" + pxRobotRole + "'" + LS + " pref_" + j + "_pxRobotRenewalFlag : '" + pxRobotRenewalFlag + "'" + LS + " pref_" + j + "_pxUserProxy : '" + pxUserProxy + "'" + LS + " pref_" + j + "_softwareTags : '" + softwareTags + "'" + LS; } // for each preference infrastructure String jobRequirements = appInitPreferences.getJobRequirements(); String pilotScript = appInitPreferences.getPilotScript(); prefs.setValue("pref_jobRequirements", jobRequirements); prefs.setValue("pref_pilotScript", pilotScript); storedPrefs += "pref_jobRequirements: '" + jobRequirements + "'" + LS + "pref_pilotScript : '" + pilotScript + "'" + LS; // Store preferences prefs.store(); } // pref !=null // Show saved preferences _log.info("Stored preferences" + LS + "------------------" + storedPrefs + LS); } // storePreferences /** * This method fills the appPreferences values retrieving them frorm the * portlet preference object. * This method can be called by both processAction or doView methods * in case no preference values are yet defined the default settings loaded * by the init method will be used * * @param actionRequest an ActionRequest instance or, * @param renderRequest a RenderRequest instance * */ private void getPreferences(ActionRequest actionRequest, RenderRequest renderRequest) { _log.info("Calling: getPreferences ..."); PortletPreferences prefs = null; if (null != actionRequest) prefs = actionRequest.getPreferences(); else if (null != renderRequest) prefs = renderRequest.getPreferences(); else _log.warn("Both render request and action request are null"); if (null != prefs) { appPreferences.updateValue("logLevel", "" + prefs.getValue("pref_logLevel", appInitPreferences.getLogLevel())); appPreferences.updateValue("gridOperationId", "" + prefs.getValue("pref_gridOperationId", appInitPreferences.getGridOperationId())); appPreferences.updateValue("gridOperationDesc", "" + prefs.getValue("pref_gridOperationDesc", appInitPreferences.getGridOperationDesc())); appPreferences.updateValue("numInfrastructures", "" + prefs.getValue("pref_numInfrastructures", "" + appInitPreferences.getNumInfrastructures())); // Now retrieves the infrastructures information int numInfras = appPreferences.getNumInfrastructures(); _log.info("getpref: num infra=" + numInfras); // For each infrastructure ... // The preference name is indexed with the infrastructure number: 1,2,... String infrastructuresInfrormations = ""; for (int i = 0; i < numInfras; i++) { int j = i + 1; int k = appInitPreferences.getNumInfrastructures(); appPreferences.updateInfrastructureValue(i, "enableInfrastructure", "" + prefs.getValue("pref_" + j + "_enableInfrastructure", (i < k) ? appInitPreferences.getEnableInfrastructure(i) : "")); appPreferences.updateInfrastructureValue(i, "nameInfrastructure", "" + prefs.getValue("pref_" + j + "_nameInfrastructure", (i < k) ? appInitPreferences.getNameInfrastructure(i) : "")); appPreferences.updateInfrastructureValue(i, "acronymInfrastructure", "" + prefs.getValue("pref_" + j + "_acronymInfrastructure", (i < k) ? appInitPreferences.getAcronymInfrastructure(i) : "")); appPreferences.updateInfrastructureValue(i, "bdiiHost", "" + prefs .getValue("pref_" + j + "_bdiiHost", (i < k) ? appInitPreferences.getBdiiHost(i) : "")); appPreferences.updateInfrastructureValue(i, "wmsHosts", "" + prefs .getValue("pref_" + j + "_wmsHosts", (i < k) ? appInitPreferences.getWmsHosts(i) : "")); appPreferences.updateInfrastructureValue(i, "pxServerHost", "" + prefs.getValue("pref_" + j + "_pxServerHost", (i < k) ? appInitPreferences.getPxServerHost(i) : "")); appPreferences.updateInfrastructureValue(i, "pxServerPort", "" + prefs.getValue("pref_" + j + "_pxServerPort", (i < k) ? appInitPreferences.getPxServerPort(i) : "")); appPreferences.updateInfrastructureValue(i, "pxServerSecure", "" + prefs.getValue("pref_" + j + "_pxServerSecure", (i < k) ? appInitPreferences.getPxServerSecure(i) : "")); appPreferences.updateInfrastructureValue(i, "pxRobotId", "" + prefs .getValue("pref_" + j + "_pxRobotId", (i < k) ? appInitPreferences.getPxRobotId(i) : "")); appPreferences.updateInfrastructureValue(i, "pxRobotVO", "" + prefs .getValue("pref_" + j + "_pxRobotVO", (i < k) ? appInitPreferences.getPxRobotVO(i) : "")); appPreferences.updateInfrastructureValue(i, "pxRobotRole", "" + prefs.getValue("pref_" + j + "_pxRobotRole", (i < k) ? appInitPreferences.getPxRobotRole(i) : "")); appPreferences.updateInfrastructureValue(i, "pxRobotRenewalFlag", "" + prefs.getValue("pref_" + j + "_pxRobotRenewalFlag", (i < k) ? appInitPreferences.getPxRobotRenewalFlag(i) : "")); appPreferences.updateInfrastructureValue(i, "pxUserProxy", "" + prefs.getValue("pref_" + j + "_pxUserProxy", (i < k) ? appInitPreferences.getPxUserProxy(i) : "")); appPreferences.updateInfrastructureValue(i, "softwareTags", "" + prefs.getValue("pref_" + j + "_softwareTags", (i < k) ? appInitPreferences.getSoftwareTags(i) : "")); _log.info("dump: " + LS + appPreferences.dumpInfrastructure(i)); } // for each Infrastructure appPreferences.updateValue("jobRequirements", "" + prefs.getValue("pref_jobRequirements", appInitPreferences.getJobRequirements())); appPreferences.updateValue("pilotScript", "" + prefs.getValue("pref_pilotScript", appInitPreferences.getPilotScript())); // Assigns the log level _log.setLogLevel(appPreferences.getLogLevel()); // Show preference values into log _log.info(appPreferences.dump()); } // if } // getPreferences /** * This method takes as input a filename and will transfer its content inside a String variable * * @param file A complete path to a given file * @return File content into a String * @throws IOException */ private String updateString(String file) throws IOException { String line; StringBuilder stringBuilder = new StringBuilder(); BufferedReader reader = new BufferedReader(new FileReader(file)); while ((line = reader.readLine()) != null) { stringBuilder.append(line); stringBuilder.append(LS); } return stringBuilder.toString(); } /** * This method will transfer the content of a given String into a given filename * * @param fileName A complete path to a file to write * @param fileContent The string content of the file to write * @throws IOException */ private void storeString(String fileName, String fileContent) throws IOException { BufferedWriter writer = new BufferedWriter(new FileWriter(fileName)); writer.write(fileContent); writer.close(); } /** * This enumerated type contains all JSP input items to be managed * by the getInputForm method * * @see getInputForm */ private enum inputControlsIds { file_inputFile // Input file textarea , inputFile // Input file input file , JobIdentifier // User defined Job identifier }; /** * This method manages the user input fields managing two cases * distinguished by the type of the input <form ... statement * The use of upload file controls needs the use of "multipart/form-data" * while the else condition of the isMultipartContent check manages the * standard input case. The multipart content needs a manual processing of * all <form items * All form' input items are identified by the 'name' input property * inside the jsp file * * @param request ActionRequest instance (processAction) * @param appInput AppInput instance storing the jobSubmission data */ void getInputForm(ActionRequest request, AppInput appInput) { if (PortletFileUpload.isMultipartContent(request)) try { FileItemFactory factory = new DiskFileItemFactory(); PortletFileUpload upload = new PortletFileUpload(factory); List items = upload.parseRequest(request); File repositoryPath = new File("/tmp"); DiskFileItemFactory diskFileItemFactory = new DiskFileItemFactory(); diskFileItemFactory.setRepository(repositoryPath); Iterator iter = items.iterator(); String logstring = ""; while (iter.hasNext()) { FileItem item = (FileItem) iter.next(); String fieldName = item.getFieldName(); String fileName = item.getName(); String contentType = item.getContentType(); boolean isInMemory = item.isInMemory(); long sizeInBytes = item.getSize(); // Prepare a log string with field list logstring += LS + "field name: '" + fieldName + "' - '" + item.getString() + "'"; switch (inputControlsIds.valueOf(fieldName)) { case file_inputFile: appInput.inputFileName = item.getString(); processInputFile(item, appInput); break; case inputFile: appInput.inputFileText = item.getString(); break; case JobIdentifier: appInput.jobIdentifier = item.getString(); break; default: _log.warn("Unhandled input field: '" + fieldName + "' - '" + item.getString() + "'"); } // switch fieldName } // while iter.hasNext() _log.info(LS + "Reporting" + LS + "---------" + LS + logstring + LS); } // try catch (Exception e) { _log.info("Caught exception while processing files to upload: '" + e.toString() + "'"); } // The input form do not use the "multipart/form-data" else { // Retrieve from the input form the given application values appInput.inputFileName = (String) request.getParameter("file_inputFile"); appInput.inputFileText = (String) request.getParameter("inputFile"); appInput.jobIdentifier = (String) request.getParameter("JobIdentifier"); } // ! isMultipartContent // Show into the log the taken inputs _log.info(LS + "Taken input parameters:" + LS + "-----------------------" + LS + "inputFileName: '" + appInput.inputFileName + "'" + LS + "inputFileText: '" + appInput.inputFileText + "'" + LS + "jobIdentifier: '" + appInput.jobIdentifier + "'" + LS); } // getInputForm /** * This method is called when the user specifies a input file to upload * The file will be saved first into /tmp directory and then its content * stored into the corresponding String variable * Before to submit the job the String value will be stored in the * proper job inputSandbox file * * @param item * @param appInput AppInput instance storing the jobSubmission data */ void processInputFile(FileItem item, AppInput appInput) { // Determin the filename String fileName = item.getName(); if (!fileName.equals("")) { // Determine the fieldName String fieldName = item.getFieldName(); // Create a filename for the uploaded file String theNewFileName = "/tmp/" + appInput.timestamp + "_" + appInput.username + "_" + fileName; File uploadedFile = new File(theNewFileName); _log.info("Uploading file: '" + fileName + "' into '" + theNewFileName + "'"); try { item.write(uploadedFile); } catch (Exception e) { _log.error("Caught exception while uploading file: 'file_inputFile'"); } // File content has to be inserted into a String variables: // inputFileName -> inputFileText try { if (fieldName.equals("file_inputFile")) appInput.inputFileText = updateString(theNewFileName); // Other params can be added as below ... //else if(fieldName.equals("...")) // ...=updateString(theNewFileName); else { // Never happens } } catch (Exception e) { _log.error("Caught exception while processing strings: '" + e.toString() + "'"); } } // if } // processInputFile /** * Before to submit the job this method creates the inputSandbox files * starting from users' input fields (textareas or uploaded files) * * @param appInput AppInput instance storing the jobSubmission data */ void updateFiles(AppInput appInput) { // First of all remomve all possible ^Ms from Strings appInput.inputFileText = appInput.inputFileText.replaceAll("\r", ""); // Now save string content into files // This must be done for each input sandbox file try { appInput.inputSandbox_inputFile = "/tmp/" + appInput.timestamp + "_" + appInput.username + "_input_file.txt"; FileWriter fwInput = new FileWriter(appInput.inputSandbox_inputFile); BufferedWriter bwInput = new BufferedWriter(fwInput); bwInput.write(appInput.inputFileText); bwInput.close(); } catch (Exception e) { _log.error("Caught exception while creating inputSandbox files"); } } // updateFiles /** * This method sends the job into the distributed infrastructure using * the GridEngine methods * * @param appInput AppInput instance storing the jobSubmission data */ void submitJob(AppInput appInput) { // // Initialize the GridEngine Multi Infrastructure Job Submission object // MultiInfrastructureJobSubmission miJobSubmission = new MultiInfrastructureJobSubmission(); // Assigns all enabled infrastructures InfrastructureInfo[] infrastructuresInfo = appPreferences.getEnabledInfrastructures(); for (int i = 0; i < infrastructuresInfo.length; i++) { _log.info("Adding infrastructure #" + (i + 1) + " - Name: '" + infrastructuresInfo[i].getName() + "'" + LS); miJobSubmission.addInfrastructure(infrastructuresInfo[i]); } // Check the enabled infrastructures if (infrastructuresInfo.length > 0) { // Application Id int applicationId = Integer.parseInt(appPreferences.getGridOperationId()); // Grid Engine' UserTraking needs the portal IP address String portalIPAddress = ""; try { InetAddress addr = InetAddress.getLocalHost(); byte[] ipAddr = addr.getAddress(); portalIPAddress = "" + ipAddr[0] + ":" + ipAddr[1] + ":" + ipAddr[2] + ":" + ipAddr[3]; } catch (Exception e) { _log.error("Unable to get the portal IP address"); } // Job details String executable = "/bin/sh"; // Application executable String arguments = appPreferences.getPilotScript(); // executable' arguments String outputPath = "/tmp/"; // Output Path String outputFile = "g-hmmer-Output.txt"; // Distributed application standard output String errorFile = "g-hmmer-Error.txt"; // Distrubuted application standard error String appFile = "g-hmmer-Files.tar.gz"; // Hostname output files (created by the pilot script) // InputSandbox (string with comma separated list of file names) /*String inputSandbox=appServerPath+"WEB-INF/job/" // +appPreferences.getPilotScript() // pilot script +","+appInput.inputSandbox_inputFile // input file ; */ String inputSandbox = appServerPath + "/WEB-INF/job/pilot_script.sh ," + appServerPath + "/WEB-INF/job/hmmer-2.3.2.tar.gz ," + appServerPath + "/WEB-INF/job/secuencia.fasta ," + appServerPath + "/WEB-INF/job/secuenciah.hmm"; // OutputSandbox (string with comma separated list of file names) String outputSandbox = appFile; // Output file // Take care of job requirements // More requirements can be specified in the preference value 'jobRequirements' // separating each requirement by the ';' character String jdlRequirements[] = appPreferences.getJobRequirements().split(";"); int numRequirements = 0; for (int i = 0; i < jdlRequirements.length; i++) { if (!jdlRequirements[i].equals("")) { jdlRequirements[numRequirements] = "JDLRequirements=(" + jdlRequirements[i] + ")"; numRequirements++; _log.info("Requirement[" + i + "]='" + jdlRequirements[i] + "'"); } } // for each jobRequirement // Other job initialization settings miJobSubmission.setExecutable(executable); // Specify the executeable miJobSubmission.setArguments(arguments); // Specify the application' arguments miJobSubmission.setOutputPath(outputPath); // Specify the output directory miJobSubmission.setOutputFiles(outputSandbox); // Setup output files (OutputSandbox) miJobSubmission.setJobOutput(outputFile); // Specify the std-outputr file miJobSubmission.setJobError(errorFile); // Specify the std-error file if (null != inputSandbox // Setup input files (InputSandbox) avoiding empty inputSandboxes && inputSandbox.length() > 0) miJobSubmission.setInputFiles(inputSandbox); if (numRequirements > 0) // Setup the JDL requirements miJobSubmission.setJDLRequirements(jdlRequirements); // Submit Job miJobSubmission.submitJobAsync(appInput.username, portalIPAddress, applicationId, appInput.jobIdentifier); // Show log // View jobSubmission details in the log _log.info(LS + "JobSent" + LS + "-------" + LS + "Portal address: '" + portalIPAddress + "'" + LS + "Executable : '" + executable + "'" + LS + "Arguments : '" + arguments + "'" + LS + "Output path : '" + outputPath + "'" + LS + "Output sandbox: '" + outputSandbox + "'" + LS + "Ouput file : '" + outputFile + "'" + LS + "Error file : '" + errorFile + "'" + LS + "Input sandbox : '" + inputSandbox + "'" + LS); // _log.info } // numInfra > 0 else { _log.warn(LS + "There are no enough enabled infrastructures!" + LS + "It is impossible to send any job" + LS + "Configure the application preferences in order to setup" + LS + "or enable at least one infrastructure." + LS); } // numInfra == 0 } // submitJob } // g_hmmer_portlet