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Revert "Merged Staging & Custom look (#155)"
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,147 +1,147 @@ | ||
| <%-- | ||
| * GIGWA - Genotype Investigator for Genome Wide Analyses | ||
| * Copyright (C) 2016 - 2019, <CIRAD> <IRD> | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify it under | ||
| * the terms of the GNU Affero General Public License, version 3 as published by | ||
| * the Free Software Foundation. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | ||
| * FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more | ||
| * details. | ||
| * | ||
| * See <http://www.gnu.org/licenses/agpl.html> for details about GNU General | ||
| * Public License V3. | ||
| --%> | ||
| <%@ page language="java" contentType="text/html; charset=utf-8" pageEncoding="UTF-8" import="fr.cirad.web.controller.gigwa.GigwaRestController"%> | ||
| <%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %> | ||
| <%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions"%> | ||
| <jsp:useBean id="appConfig" class="fr.cirad.tools.AppConfig" /> | ||
|
|
||
| <html> | ||
|
|
||
| <head> | ||
| <script type="text/javascript" src="js/jquery-1.12.4.min.js"></script> | ||
| <script type="text/javascript" src="js/bootstrap.min.js"></script> | ||
| <script type="text/javascript" src="<c:url value="/js/common.js" />"></script> | ||
| <link rel="shortcut icon" href="images/favicon.png" type="image/x-icon" /> | ||
| <link type="text/css" rel="stylesheet" href="css/bootstrap.min.css"> | ||
| <link type="text/css" rel="stylesheet" href="css/main.css"> | ||
| <script type="text/javascript"> | ||
| var progressUrl = "<c:url value='<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.PROGRESS_PATH%>' />"; | ||
| var abortUrl = "<c:url value='<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.ABORT_PROCESS_PATH%>' />"; | ||
| var downloadURL = "${param.successURL}"; | ||
| var fileName = downloadURL.substring(downloadURL.lastIndexOf("/") + 1); | ||
| if (fileName.startsWith("?")) | ||
| fileName = location.origin + '<c:url value='/' />' + fileName; | ||
| var processAborted = false; | ||
| <c:if test="${param.exportFormat != null}"> | ||
| var galaxyPushURL = '<c:url value="<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.GALAXY_HISTORY_PUSH%>" />'; | ||
| var onlineOutputTools = null; | ||
| var igvDataLoadPort, igvGenomeListUrl; | ||
| <c:set var="igvDataLoadPort" value="<%= appConfig.get(\"igvDataLoadPort\") %>"></c:set> | ||
| <c:set var="igvGenomeListUrl" value="<%= appConfig.get(\"igvGenomeListUrl\") %>"></c:set> | ||
| <c:if test='${!fn:startsWith(igvDataLoadPort, "??") && !empty igvDataLoadPort && !fn:startsWith(igvGenomeListUrl, "??") && !empty igvGenomeListUrl}'> | ||
| igvDataLoadPort = ${igvDataLoadPort}; | ||
| igvGenomeListUrl = '<c:url value="<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.IGV_GENOME_LIST_URL %>" />'; | ||
| </c:if> | ||
| $.ajax({ | ||
| url: '<c:url value="<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.ONLINE_OUTPUT_TOOLS_URL%>" />', | ||
| async: true, | ||
| type: "GET", | ||
| contentType: "application/json;charset=utf-8", | ||
| success: function(labelsAndURLs) { | ||
| onlineOutputTools = labelsAndURLs; | ||
| onlineOutputTools["Custom tool"] = {"url" : "", "formats" : ""}; | ||
| }, | ||
| error: function(xhr, thrownError) { | ||
| handleError(xhr, thrownError); | ||
| } | ||
| }); | ||
| </c:if> | ||
| function watchProgress() | ||
| { | ||
| $.ajax({ | ||
| url: progressUrl<c:if test="${param.process != null}">+'?progressToken=${param.process}'</c:if>, | ||
| type: "GET", | ||
| async: false, | ||
| <c:if test="${param.token != null}">headers: { "Authorization": "Bearer ${param.token}" },</c:if> | ||
| success: function (jsonResult) { | ||
| if (jsonResult == null) { | ||
| $('body').append('<center id="defaultMsg"><p style="margin-top:60px;" class="bold">No such process is running at the moment.</p><p>Refresh to try again or use the link below to access resulting data in case the process has already finished:<br/><br/><a style="cursor:pointer;" href="' + downloadURL + '">' + (fileName == '?' ? downloadURL : fileName) + '</a></p></center>'); | ||
| <c:if test="${param.exportFormat != null}"> | ||
| $.ajax({ | ||
| type: 'HEAD', | ||
| url: downloadURL, | ||
| success: function(data, textStatus, jqXHR) { | ||
| if (jqXHR.status >= 200 && jqXHR.status < 300) { | ||
| successFunction(); | ||
| $("#defaultMsg").remove(); | ||
| } | ||
| } | ||
| }); | ||
| </c:if> | ||
| } | ||
| else | ||
| { | ||
| $('#progress').modal({backdrop: 'static', keyboard: false, show: true}); | ||
| $('.modal-backdrop.in').css('opacity', '0.1'); | ||
| displayProcessProgress(5, <c:choose><c:when test="${param.token != null}">'${param.token}'</c:when><c:otherwise>null</c:otherwise></c:choose>, '${param.process}'<c:if test="${param.exportFormat != null}">, successFunction</c:if>); | ||
| $('#progress').on('hidden.bs.modal', function () { | ||
| if (processAborted) | ||
| $('body').append('<center><p style="margin-top:60px;" class="bold">Process aborted</p></center>'); | ||
| <c:if test="${param.exportFormat == null}"> | ||
| else if (!$('#progress').data('error')) | ||
| $('body').append('<center><p style="margin-top:60px;" class="bold">Process has completed. Data is now <a style="cursor:pointer;" href="' + downloadURL + '">available here</a></center>'); | ||
| </c:if> | ||
| $('#progress').off('hidden.bs.modal'); | ||
| }); | ||
| } | ||
| }, | ||
| error: function (xhr, ajaxOptions, thrownError) { | ||
| handleError(xhr, thrownError); | ||
| } | ||
| }); | ||
| $("div.modal-backdrop").remove(); | ||
| } | ||
| <c:if test="${param.exportFormat != null}"> | ||
| function successFunction() { | ||
| let fileExtensions = "${param.exportFormatExtensions}".split(";"); | ||
| <c:if test="${param.exportedTsvMetadata eq true}"> | ||
| fileExtensions.push("tsv"); | ||
| </c:if> | ||
| showServerExportBox(${param.keepExportOnServ}, fileExtensions); | ||
| } | ||
| </c:if> | ||
| </script> | ||
| <title>Gigwa process watcher</title> | ||
| </head> | ||
| <body style='background-color:#f0f0f0;' onload="$('button#abort').css('display', ${param.abortable eq 'true'} ? 'inline' : 'none'); watchProgress();"> | ||
| <c:if test="${param.exportFormat != null}"> | ||
| <input type="hidden" id="exportFormat" value="${param.exportFormat}" /> | ||
| <input type="hidden" id="module" value="${param.module}" /> | ||
| <input type="hidden" id="galaxyInstanceURL" value="${param.galaxyInstanceUrl}" /> | ||
| <input type="hidden" id="exportedIndividualCount" value="${param.exportedIndividualCount}" /> | ||
| <input type="hidden" id="count" value="${param.exportedVariantCount}" /> | ||
| </c:if> | ||
| <div style='background-color:white; width:100%; padding:5px;'><img src="<c:url value='/images/logo.png' />" height="25"></div> | ||
| <div id='progress' style='margin-top:50px; margin-left:20%; width:60%; display:block; text-align:center; display:none;'> | ||
| <p>This process is running as a background task.</p> | ||
| <p>You may leave the main Gigwa page and either keep this one open or copy its URL to check again later.</p> | ||
| <h2 id="progressText" class="loading-message" style='margin-top:100px'>Please wait...</h2> | ||
| <button class="btn btn-danger btn-sm" id="abort" style="display:none;" type="button" name="abort" onclick="if (confirm('Are you sure?')) abort('${param.process}');">Abort</button> | ||
| </div> | ||
| <div id="serverExportBox" class="panel" style="position:absolute; margin:0; top:50px; left:calc(50% - 250px); width:400px;"></div> | ||
| </body> | ||
| <%-- | ||
| * GIGWA - Genotype Investigator for Genome Wide Analyses | ||
| * Copyright (C) 2016 - 2019, <CIRAD> <IRD> | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify it under | ||
| * the terms of the GNU Affero General Public License, version 3 as published by | ||
| * the Free Software Foundation. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | ||
| * FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more | ||
| * details. | ||
| * | ||
| * See <http://www.gnu.org/licenses/agpl.html> for details about GNU General | ||
| * Public License V3. | ||
| --%> | ||
| <%@ page language="java" contentType="text/html; charset=utf-8" pageEncoding="UTF-8" import="fr.cirad.web.controller.gigwa.GigwaRestController"%> | ||
| <%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %> | ||
| <%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions"%> | ||
| <jsp:useBean id="appConfig" class="fr.cirad.tools.AppConfig" /> | ||
|
|
||
| <html> | ||
|
|
||
| <head> | ||
| <script type="text/javascript" src="js/jquery-1.12.4.min.js"></script> | ||
| <script type="text/javascript" src="js/bootstrap.min.js"></script> | ||
| <script type="text/javascript" src="<c:url value="/js/common.js" />"></script> | ||
| <link rel="shortcut icon" href="images/favicon.png" type="image/x-icon" /> | ||
| <link type="text/css" rel="stylesheet" href="css/bootstrap.min.css"> | ||
| <link type="text/css" rel="stylesheet" href="css/main.css"> | ||
| <script type="text/javascript"> | ||
| var progressUrl = "<c:url value='<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.PROGRESS_PATH%>' />"; | ||
| var abortUrl = "<c:url value='<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.ABORT_PROCESS_PATH%>' />"; | ||
| var downloadURL = "${param.successURL}"; | ||
| var fileName = downloadURL.substring(downloadURL.lastIndexOf("/") + 1); | ||
| if (fileName.startsWith("?")) | ||
| fileName = location.origin + '<c:url value='/' />' + fileName; | ||
| var processAborted = false; | ||
| <c:if test="${param.exportFormat != null}"> | ||
| var galaxyPushURL = '<c:url value="<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.GALAXY_HISTORY_PUSH%>" />'; | ||
| var onlineOutputTools = null; | ||
| var igvDataLoadPort, igvGenomeListUrl; | ||
| <c:set var="igvDataLoadPort" value="<%= appConfig.get(\"igvDataLoadPort\") %>"></c:set> | ||
| <c:set var="igvGenomeListUrl" value="<%= appConfig.get(\"igvGenomeListUrl\") %>"></c:set> | ||
| <c:if test='${!fn:startsWith(igvDataLoadPort, "??") && !empty igvDataLoadPort && !fn:startsWith(igvGenomeListUrl, "??") && !empty igvGenomeListUrl}'> | ||
| igvDataLoadPort = ${igvDataLoadPort}; | ||
| igvGenomeListUrl = '<c:url value="<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.IGV_GENOME_LIST_URL %>" />'; | ||
| </c:if> | ||
| $.ajax({ | ||
| url: '<c:url value="<%=GigwaRestController.REST_PATH + GigwaRestController.BASE_URL + GigwaRestController.ONLINE_OUTPUT_TOOLS_URL%>" />', | ||
| async: true, | ||
| type: "GET", | ||
| contentType: "application/json;charset=utf-8", | ||
| success: function(labelsAndURLs) { | ||
| onlineOutputTools = labelsAndURLs; | ||
| onlineOutputTools["Custom tool"] = {"url" : "", "formats" : ""}; | ||
| }, | ||
| error: function(xhr, thrownError) { | ||
| handleError(xhr, thrownError); | ||
| } | ||
| }); | ||
| </c:if> | ||
| function watchProgress() | ||
| { | ||
| $.ajax({ | ||
| url: progressUrl<c:if test="${param.process != null}">+'?progressToken=${param.process}'</c:if>, | ||
| type: "GET", | ||
| async: false, | ||
| <c:if test="${param.token != null}">headers: { "Authorization": "Bearer ${param.token}" },</c:if> | ||
| success: function (jsonResult) { | ||
| if (jsonResult == null) { | ||
| $('body').append('<center id="defaultMsg"><p style="margin-top:60px;" class="bold">No such process is running at the moment.</p><p>Refresh to try again or use the link below to access resulting data in case the process has already finished:<br/><br/><a style="cursor:pointer;" href="' + downloadURL + '">' + (fileName == '?' ? downloadURL : fileName) + '</a></p></center>'); | ||
| <c:if test="${param.exportFormat != null}"> | ||
| $.ajax({ | ||
| type: 'HEAD', | ||
| url: downloadURL, | ||
| success: function(data, textStatus, jqXHR) { | ||
| if (jqXHR.status >= 200 && jqXHR.status < 300) { | ||
| successFunction(); | ||
| $("#defaultMsg").remove(); | ||
| } | ||
| } | ||
| }); | ||
| </c:if> | ||
| } | ||
| else | ||
| { | ||
| $('#progress').modal({backdrop: 'static', keyboard: false, show: true}); | ||
| $('.modal-backdrop.in').css('opacity', '0.1'); | ||
| displayProcessProgress(5, <c:choose><c:when test="${param.token != null}">'${param.token}'</c:when><c:otherwise>null</c:otherwise></c:choose>, '${param.process}'<c:if test="${param.exportFormat != null}">, successFunction</c:if>); | ||
| $('#progress').on('hidden.bs.modal', function () { | ||
| if (processAborted) | ||
| $('body').append('<center><p style="margin-top:60px;" class="bold">Process aborted</p></center>'); | ||
| <c:if test="${param.exportFormat == null}"> | ||
| else if (!$('#progress').data('error')) | ||
| $('body').append('<center><p style="margin-top:60px;" class="bold">Process has completed. Data is now <a style="cursor:pointer;" href="' + downloadURL + '">available here</a></center>'); | ||
| </c:if> | ||
| $('#progress').off('hidden.bs.modal'); | ||
| }); | ||
| } | ||
| }, | ||
| error: function (xhr, ajaxOptions, thrownError) { | ||
| handleError(xhr, thrownError); | ||
| } | ||
| }); | ||
| $("div.modal-backdrop").remove(); | ||
| } | ||
| <c:if test="${param.exportFormat != null}"> | ||
| function successFunction() { | ||
| let fileExtensions = "${param.exportFormatExtensions}".split(";"); | ||
| <c:if test="${param.exportedTsvMetadata eq true}"> | ||
| fileExtensions.push("tsv"); | ||
| </c:if> | ||
| showServerExportBox(${param.keepExportOnServ}, fileExtensions); | ||
| } | ||
| </c:if> | ||
| </script> | ||
| <title>Gigwa process watcher</title> | ||
| </head> | ||
| <body style='background-color:#f0f0f0;' onload="$('button#abort').css('display', ${param.abortable eq 'true'} ? 'inline' : 'none'); watchProgress();"> | ||
| <c:if test="${param.exportFormat != null}"> | ||
| <input type="hidden" id="exportFormat" value="${param.exportFormat}" /> | ||
| <input type="hidden" id="module" value="${param.module}" /> | ||
| <input type="hidden" id="galaxyInstanceURL" value="${param.galaxyInstanceUrl}" /> | ||
| <input type="hidden" id="exportedIndividualCount" value="${param.exportedIndividualCount}" /> | ||
| <input type="hidden" id="count" value="${param.exportedVariantCount}" /> | ||
| </c:if> | ||
| <div style='background-color:white; width:100%; padding:5px;'><img src="<c:url value='/images/logo.png' />" height="25"></div> | ||
| <div id='progress' style='margin-top:50px; margin-left:20%; width:60%; display:block; text-align:center; display:none;'> | ||
| <p>This process is running as a background task.</p> | ||
| <p>You may leave the main Gigwa page and either keep this one open or copy its URL to check again later.</p> | ||
| <h2 id="progressText" class="loading-message" style='margin-top:100px'>Please wait...</h2> | ||
| <button class="btn btn-danger btn-sm" id="abort" style="display:none;" type="button" name="abort" onclick="if (confirm('Are you sure?')) abort('${param.process}');">Abort</button> | ||
| </div> | ||
| <div id="serverExportBox" class="panel" style="position:absolute; margin:0; top:50px; left:calc(50% - 250px); width:400px;"></div> | ||
| </body> | ||
| </html> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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