From 916f48aa3aca2a0d01eda2ad72f54e9af22b6724 Mon Sep 17 00:00:00 2001
From: Rick Herrick <jrherrick@wustl.edu>
Date: Fri, 8 Apr 2016 18:28:56 -0500
Subject: [PATCH] Changes to support spawner functionality.
---
build.gradle | 1 +
.../xnat/archive/GradualDicomImporter.java | 1 +
.../configuration/WebConfig.java | 2 +-
.../controllers/ManageElementsController.java | 58 ++
src/main/webapp/WEB-INF/conf/mq-context.xml | 2 +-
.../webapp/WEB-INF/tags/spawner/layout.tag | 764 ++++++++++++++++++
.../webapp/WEB-INF/views/spawner/element.jsp | 0
.../webapp/WEB-INF/views/spawner/elements.jsp | 257 ++++++
8 files changed, 1083 insertions(+), 2 deletions(-)
rename src/main/java/org/nrg/{xapi => xnat}/configuration/WebConfig.java (98%)
create mode 100644 src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java
create mode 100644 src/main/webapp/WEB-INF/tags/spawner/layout.tag
create mode 100644 src/main/webapp/WEB-INF/views/spawner/element.jsp
create mode 100644 src/main/webapp/WEB-INF/views/spawner/elements.jsp
diff --git a/build.gradle b/build.gradle
index 5e6307de..8b3159eb 100644
--- a/build.gradle
+++ b/build.gradle
@@ -221,6 +221,7 @@ configurations {
dependencies {
// NRG dependencies first.
+ compile "org.nrg.xnat:spawner:${vXnat}"
compile "org.nrg.xdat:core:${vXnat}"
compile "org.nrg:framework:${vXnat}"
compile "org.nrg:transaction:${vXnat}"
diff --git a/src/main/java/org/nrg/xnat/archive/GradualDicomImporter.java b/src/main/java/org/nrg/xnat/archive/GradualDicomImporter.java
index 621f883a..f1cfb0c0 100644
--- a/src/main/java/org/nrg/xnat/archive/GradualDicomImporter.java
+++ b/src/main/java/org/nrg/xnat/archive/GradualDicomImporter.java
@@ -361,6 +361,7 @@ public class GradualDicomImporter extends ImporterHandlerA {
//
// This record is necessary so that, if this row was created by this call, it can be deleted if anonymization
// goes wrong. In case of any other error the file is left on the filesystem.
+ // TODO: This is where things are going awry with Jenny's prearchive bug.
Either<SessionData, SessionData> getOrCreate;
try {
getOrCreate = PrearcDatabase.eitherGetOrCreateSession(session, tsdir, shouldAutoArchive(project, dicom));
diff --git a/src/main/java/org/nrg/xapi/configuration/WebConfig.java b/src/main/java/org/nrg/xnat/configuration/WebConfig.java
similarity index 98%
rename from src/main/java/org/nrg/xapi/configuration/WebConfig.java
rename to src/main/java/org/nrg/xnat/configuration/WebConfig.java
index 5cb9a698..d2e4900f 100644
--- a/src/main/java/org/nrg/xapi/configuration/WebConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/WebConfig.java
@@ -1,4 +1,4 @@
-package org.nrg.xapi.configuration;
+package org.nrg.xnat.configuration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java b/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java
new file mode 100644
index 00000000..2b2ad5a8
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/spawner/controllers/ManageElementsController.java
@@ -0,0 +1,58 @@
+package org.nrg.xnat.spawner.controllers;
+
+import org.apache.commons.lang3.StringUtils;
+import org.nrg.xnat.spawner.entities.SpawnerElement;
+import org.nrg.xnat.spawner.exceptions.InvalidElementIdException;
+import org.nrg.xnat.spawner.services.SpawnerService;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.servlet.ModelAndView;
+
+import javax.inject.Inject;
+
+@Controller
+@RequestMapping(value = "/spawner/elements", produces = "application/json")
+public class ManageElementsController {
+
+ @RequestMapping
+ public ModelAndView getAvailableElements() {
+ return new ModelAndView("spawner/elements", "elements", _service.getAvailableSpawnerElementIds());
+ }
+
+ @RequestMapping(value = "{elementId}", method = RequestMethod.GET)
+ public ModelAndView getElement(@PathVariable final String elementId) {
+ final SpawnerElement element = _service.retrieve(elementId);
+ return new ModelAndView("spawner/element", element == null ? "error" : "element", element == null ? "The ID element " + elementId + " was not found in the system." : element);
+ }
+
+ @RequestMapping(value = "{elementId}", method = RequestMethod.PUT)
+ public ModelAndView setElement(@PathVariable final String elementId, @RequestBody final SpawnerElement element) {
+ if (element == null) {
+ return new ModelAndView("spawner/element", "error", "No valid spawner element was found in your submitted data.");
+ }
+ final SpawnerElement existing = _service.retrieve(elementId);
+ final boolean isModElementId = !StringUtils.equals(existing.getElementId(), element.getElementId());
+ final boolean isModYaml = !StringUtils.equals(existing.getYaml(), element.getYaml());
+ if (isModElementId || isModYaml) {
+ if (isModElementId) {
+ try {
+ existing.setElementId(element.getElementId());
+ } catch (InvalidElementIdException e) {
+ return new ModelAndView("spawner/element", "error", "The element ID " + element.getElementId() + " in your submitted data is invalid. Check for duplicated or invalid values.");
+ }
+ }
+ if (isModYaml) {
+ existing.setYaml(element.getYaml());
+ }
+ _service.update(existing);
+ return new ModelAndView("spawner/element", "element", element);
+ }
+ return new ModelAndView("spawner/element", "error", "The submitted spawner element wasn't modified, not updated.");
+ }
+
+ @Inject
+ private SpawnerService _service;
+}
diff --git a/src/main/webapp/WEB-INF/conf/mq-context.xml b/src/main/webapp/WEB-INF/conf/mq-context.xml
index a2d518e2..5e682487 100644
--- a/src/main/webapp/WEB-INF/conf/mq-context.xml
+++ b/src/main/webapp/WEB-INF/conf/mq-context.xml
@@ -24,7 +24,7 @@
<context:property-placeholder location="WEB-INF/conf/services.properties, WEB-INF/conf/services-custom.properties" ignore-resource-not-found="true" ignore-unresolvable="true" />
<!-- embedded ActiveMQ Broker -->
- <amq:broker id="activeMQBroker" brokerName="activeMQBroker" useJmx="false" persistent="true" schedulerSupport="false" >
+ <amq:broker id="activeMQBroker" brokerName="activeMQBroker" useJmx="false" persistent="true" schedulerSupport="false" useShutdownHook="false">
<amq:persistenceAdapter>
<!-- We'll use XNAT's data source, make sure the Spring ID matches. (For unit testing it's provided by the Spring test
context) Also, turning off locking, as we've no need for it with a single broker, and it was causing errors in the ActiveMQ
diff --git a/src/main/webapp/WEB-INF/tags/spawner/layout.tag b/src/main/webapp/WEB-INF/tags/spawner/layout.tag
new file mode 100644
index 00000000..5e28cd9a
--- /dev/null
+++ b/src/main/webapp/WEB-INF/tags/spawner/layout.tag
@@ -0,0 +1,764 @@
+<%@tag description="Default layout template" pageEncoding="UTF-8" %>
+<%@attribute name="title" %>
+
+<!DOCTYPE html>
+<!--[if lt IE 7]> <html class="ie ie6 ltie7 ltie8 ltie9 ltie10 no-js"> <![endif]-->
+<!--[if IE 7]> <html class="ie ie7 ltie8 ltie9 ltie10 no-js"> <![endif]-->
+<!--[if IE 8]> <html class="ie ie8 ltie9 ltie10 no-js"> <![endif]-->
+<!--[if IE 9]> <html class="ie ie9 ltie10 no-js"> <![endif]-->
+<!--[if gt IE 9]><!-->
+<html class="no-js"> <!--<![endif]-->
+
+<head>
+ <title>${title}</title>
+
+ <!-- HeaderIncludes -->
+
+ <!-- path: /xnat-templates/navigations/HeaderIncludes -->
+
+ <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
+ <meta http-equiv="Pragma" content="no-cache">
+ <meta http-equiv="cache-control" content="max-age=0">
+ <meta http-equiv="cache-control" content="no-cache">
+ <meta http-equiv="expires" content="-1">
+ <meta http-equiv="expires" content="Tue, 01 Jan 1980 1:00:00 GMT">
+
+
+ <!-- load polyfills before ANY other JavaScript -->
+ <script type="text/javascript" src="/scripts/polyfills.js"></script>
+
+ <!-- set global vars that are used often -->
+ <script type="text/javascript">
+
+ var XNAT = {};
+ var serverRoot = "";
+ var csrfToken = "66ccfc57-b8d2-4e90-8b9e-f1ff0b43e06c";
+ var showReason = typeof false != 'undefined' ? false : null;
+ var requireReason = typeof false != 'undefined' ? false : null;
+
+ </script>
+
+ <!-- XNAT global functions (no dependencies) -->
+ <script type="text/javascript" src="/scripts/globals.js"></script>
+
+ <!-- required libraries -->
+ <script>
+ // loads minified versions by default
+ // add ?debug=true to the query string
+ // or #debug to the url hash to load
+ // the non-minified versions
+ writeScripts([
+ scriptUrl('lib/loadjs/loadjs'),
+ scriptUrl('lib/jquery/jquery|.min'),
+ scriptUrl('lib/jquery/jquery-migrate-1.2.1|.min'),
+ ]);
+ </script>
+ <script type="text/javascript">
+ // use 'jq' to avoid _possible_ conflicts with Velocity
+ var jq = jQuery;
+ </script>
+
+ <!-- jQuery plugins -->
+ <link rel="stylesheet" type="text/css" href="/scripts/lib/jquery-plugins/chosen/chosen.min.css?v=1.7.0a1">
+ <script type="text/javascript" src="/scripts/lib/jquery-plugins/chosen/chosen.jquery.min.js"></script>
+ <script type="text/javascript" src="/scripts/lib/jquery-plugins/jquery.maskedinput.min.js"></script>
+ <script type="text/javascript" src="/scripts/lib/jquery-plugins/jquery.spawn.js"></script>
+
+ <!-- other libraries -->
+ <script type="text/javascript" src="/scripts/lib/spawn/spawn.js"></script>
+
+ <!-- XNAT utility functions -->
+ <script type="text/javascript" src="/scripts/utils.js"></script>
+
+ <script type="text/javascript">
+
+ /*
+ * XNAT global namespace object, which will not be overwriten if
+ * already defined. Also define some other top level namespaces.
+ */
+ extend(XNAT, {
+ /*
+ * Parent namespace that templates can use to put their
+ * own namespace
+ */
+ app: {
+ displayNames: {
+ singular: {
+ project: "Project",
+ subject: "Subject",
+ imageSession: "Session",
+ mrSession: "MR Session"
+ },
+ plural: {
+ project: "Projects",
+ subject: "Subjects",
+ imageSession: "Sessions",
+ mrSession: "MR Sessions"
+ }
+ },
+ siteId: "XNAT"
+ },
+ images: {
+ grnChk: "/images/checkmarkGreen.gif",
+ redChk: "/images/checkmarkRed.gif"
+ },
+ data: {
+ context: {
+ projectName: "",
+ projectID: "",
+ project: "",
+ xsiType: "",
+ subjectLabel: "",
+ subjectID: "",
+ label: "",
+ ID: ""
+ },
+ timestamp: jq.now() // timestamp for the page when it loads
+ }
+ });
+
+ if (XNAT.data.context.projectName === "") {
+ XNAT.data.context.projectName = "";
+ }
+
+ // 'page' object is same as 'context' - easier to remember?
+ XNAT.data.page = XNAT.data.context;
+
+ XNAT.app.showLeftBar = true;
+ XNAT.app.showLeftBarProjects = true;
+ XNAT.app.showLeftBarFavorites = true;
+ XNAT.app.showLeftBarSearch = true;
+ XNAT.app.showLeftBarBrowse = true;
+
+ window.available_elements = [];
+
+
+ window.available_elements.getByName = function (name) {
+ for (var aeC = 0; aeC < this.length; aeC++) {
+ if (this[aeC].element_name == name) {
+ return this[aeC];
+ }
+ }
+ // return empty object if not found
+ return {}
+ };
+
+
+ // quickly reference today's date
+ XNAT.data.todaysDate = {};
+ // if today was January 23, 2013...
+ // m (1), mm (01), d (23), dd (23), yyyy (2013), ISO/iso (2013-01-23), US/us (01/23/2013)
+ (function (dateObj) {
+ dateObj.date = new Date();
+ dateObj.gotMonth = dateObj.date.getMonth();
+ dateObj.m = (dateObj.gotMonth + 1).toString();
+ dateObj.mm = (dateObj.m.length === 1) ? '0' + dateObj.m : dateObj.m;
+ dateObj.d = dateObj.date.getDate().toString();
+ dateObj.dd = (dateObj.d.length === 1) ? '0' + dateObj.d : dateObj.d;
+ dateObj.yyyy = dateObj.date.getFullYear().toString();
+ dateObj.ISO = dateObj.iso = dateObj.yyyy + '-' + dateObj.mm + '-' + dateObj.dd;
+ dateObj.US = dateObj.us = dateObj.mm + '/' + dateObj.dd + '/' + dateObj.yyyy;
+ })(XNAT.data.todaysDate);
+
+ </script>
+ <script type="text/javascript">
+ // initialize "Chosen" menus on DOM load
+ // all <select class="chosen-menu"> elements
+ // will be converted
+ // putting this here to be at the top of
+ // the jQuery DOM-ready queue
+ jq(function () {
+ chosenInit()
+ });
+ </script>
+ <script type="text/javascript" src="/scripts/xdat.js"></script>
+ <script type="text/javascript" src="/scripts/DynamicJSLoad.js"></script>
+
+ <!-- YAHOO USER INTERFACE files below here -->
+ <script type="text/javascript" src="/scripts/yui/build/yahoo-dom-event/yahoo-dom-event.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/event/event-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/container/container-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/menu/menu-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/element/element-beta-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/button/button-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/connection/connection-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/treeview/treeview-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/cookie/cookie-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/tabview/tabview-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/datasource/datasource-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/resize/resize-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/dragdrop/dragdrop-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/datatable/datatable-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/paginator/paginator-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/build/json/json-min.js"></script>
+ <script type="text/javascript" src="/scripts/yui/xnat_loader.js"></script>
+ <script type="text/javascript" src="/scripts/LeftBarTreeView.js"></script>
+ <script type="text/javascript" src="/scripts/justification/justification.js"></script>
+ <script type="text/javascript">
+
+ // The YUIDOM alias is used throughout XNAT
+ var YUIDOM = YAHOO.util.Dom;
+
+ XNAT.dom = getObject(XNAT.dom || {});
+ XNAT.dom.addFormCSRF = function (__form) {
+ __form = isDefined(__form) ? $$(__form) : jq('form');
+ __form.append('<input type="hidden" name="XNAT_CSRF" value="' + csrfToken + '">')
+ };
+
+ jq(function () {
+ // add hidden input with CSRF data
+ // to all forms on page load
+ XNAT.dom.addFormCSRF();
+ });
+
+ </script>
+
+ <!-- YUI css -->
+ <link rel="stylesheet" type="text/css" href="/scripts/yui/build/assets/skins/sam/skin.css?v=1.7.0a1">
+
+ <!-- xdat.css and xnat.css loaded last to override YUI styles -->
+ <link rel="stylesheet" type="text/css" href="/style/app.css?v=1.7.0a1">
+
+ <link rel="stylesheet" type="text/css" href="/scripts/xmodal-v1/xmodal.css?v=1.7.0a1">
+ <script type="text/javascript" src="/scripts/xmodal-v1/xmodal.js"></script>
+ <script type="text/javascript" src="/scripts/xmodal-v1/xmodal-migrate.js"></script>
+
+ <link rel="stylesheet" type="text/css" href="/scripts/tabWrangler/tabWrangler.css?v=1.7.0a1">
+ <script type="text/javascript" src="/scripts/tabWrangler/tabWrangler.js"></script>
+
+ <!-- date input stuff -->
+ <link type="text/css" rel="stylesheet" href="/scripts/yui/build/calendar/assets/skins/sam/calendar.css?v=1.7.0a1">
+ <script type="text/javascript" src="/scripts/yui/build/calendar/calendar-min.js"></script>
+ <script type="text/javascript" src="/scripts/ezCalendar.js"></script>
+
+ <!-- XNAT JLAPI scripts -->
+ <script type="text/javascript" src="/scripts/xnat/url.js"></script>
+ <script type="text/javascript" src="/scripts/xnat/xhr.js"></script>
+ <script type="text/javascript" src="/scripts/xnat/ui/popup.js"></script>
+ <script type="text/javascript" src="/scripts/xnat/ui/dialog.js"></script>
+
+ <!-- /HeaderIncludes -->
+
+ <!-- path: xnat-templates/navigations/bodyOpen -->
+</head>
+<body id="page_body" class="yui-skin-sam">
+<div id="page_wrapper">
+
+ <!-- path: xdat-templates/layouts/Default -->
+
+ <!-- START: xnat-templates/navigations/DefaultTop.vm -->
+ <script type="text/javascript" src="/scripts/lib/js.cookie.js"></script>
+
+ <style type="text/css">
+ #attention_icon {
+ float: left;
+ padding-top: 7px;
+ padding-left: 11px;
+ }
+
+ #attention_icon:hover {
+ cursor: pointer;
+ }
+ </style>
+
+ <div id="user_bar">
+ <div class="inner">
+ <img id="attention_icon" src="/images/attention.png" style="display:none;"
+ alt="attention needed - click for more info" title="attention needed - click for more info">
+ <span id="user_info">Logged in as: <a
+ href="/app/template/XDATScreen_UpdateUser.vm">admin</a> <b>|</b><span
+ class="tip_icon" style="margin-right:3px;left:2px;top:3px;">
+ <span class="tip shadowed"
+ style="top:20px;z-index:10000;white-space:normal;left:-150px;width:300px;background-color:#ffc;">Your XNAT session will auto-logout after a certain period of inactivity. You can reset that timer without reloading the page by clicking "renew."</span>
+ </span>
+ Auto-logout in: <b id="timeLeft">-:--:--</b> - <a id="timeLeftRenew" href="javascript:"
+ onClick="XNAT.app.timeout.handleOk()">renew</a> <b>|</b> <a
+ id="logout_user" href="/app/action/LogoutUser">Logout</a></span>
+ <script type="text/javascript">
+ Cookies.set('guest', 'false', {path: '/'});
+ </script>
+ <div class="clear"></div>
+ </div>
+ </div><!-- /user_bar -->
+
+
+ <div id="main_nav">
+
+ <ul class="nav">
+ <!-- Sequence: 10 -->
+ <!-- allowGuest: true -->
+ <li>
+ <a id="nav-home" title="Home" href="/app/template/Index.vm"> </a>
+ <script>
+ $('#nav-home').css({
+ width: '30px',
+ backgroundImage: "url('/images/xnat-nav-logo-white-lg.png')",
+ backgroundRepeat: 'no-repeat',
+ backgroundSize: '32px',
+ backgroundPosition: 'center'
+ });
+ </script>
+ </li>
+ <!-- Sequence: 20 -->
+
+ <li><a href="#new">New</a>
+ <ul>
+ <!-- Sequence: 10 -->
+ <li><a href="/app/template/XDATScreen_add_xnat_projectData.vm">Project</a></li>
+ <!-- -->
+ <!-- -->
+ <li>
+ <a href="/app/action/XDATActionRouter/xdataction/edit/search_element/xnat%3AsubjectData">Subject</a>
+ </li>
+ <!-- -->
+
+ <!-- no object found -->
+ <!-- no object found -->
+ <!-- no object found -->
+ <!-- -->
+ <li><a href="/app/template/XDATScreen_add_experiment.vm">Experiment</a></li>
+ <!-- -->
+ <!-- -->
+ </ul>
+ </li>
+ <!-- Sequence: 30 -->
+ <li><a href="#upload">Upload</a>
+ <ul>
+ <!-- Sequence: 10 -->
+ <!-- Upload/Default -->
+ <li><a href="/app/template/LaunchUploadApplet.vm">Images</a></li>
+ <li><a href="/app/template/XMLUpload.vm">XML</a></li>
+ <li><a href="/app/template/XDATScreen_uploadCSV.vm">Spreadsheet</a></li>
+ <li><a href="/app/template/XDATScreen_prearchives.vm">Go to prearchive</a></li>
+ </ul>
+ </li>
+ <!-- Sequence: 40 -->
+
+ <li><a href="#adminbox">Administer</a>
+ <ul>
+ <!-- Sequence: 10 -->
+ <li><a href="/app/template/XDATScreen_admin.vm">Users</a></li>
+ <li><a href="/app/template/XDATScreen_groups.vm">Groups</a></li>
+ <li><a href="/app/template/XDATScreen_dataTypes.vm">Data Types</a></li>
+ <li><a href="/app/template/XDATScreen_email.vm">Email</a></li>
+ <li><a href="/app/template/XDATScreen_manage_pipeline.vm">Pipelines</a></li>
+ <li><a href="/app/template/Configuration.vm">Configuration</a></li>
+ <li><a href="/app/template/Scripts.vm">Automation</a></li>
+ <li><a href="/app/template/XDATScreen_admin_options.vm">More...</a></li>
+ </ul>
+ </li>
+
+ <!-- Title: Tools -->
+ <!-- Sequence: 50 -->
+ <!-- allowGuest: true -->
+
+ <li><a href="#tools">Tools</a>
+ <ul>
+ <!-- Sequence: 10 -->
+ <!-- allowGuest: true -->
+ <li><a href="https://wiki.xnat.org/display/XNAT16/XNAT+Desktop" target="_blank">XNAT Desktop
+ (XND)</a></li>
+ <li><a href="http://nrg.wustl.edu/projects/DICOM/DicomBrowser.jsp" target="_blank">DICOM Browser</a>
+ </li>
+ <li><a href="https://wiki.xnat.org/display/XNAT16/XNAT+Client+Tools" target="_blank">Command Prompt
+ Tools</a></li>
+ </ul>
+ </li>
+ <!-- Sequence: 60 -->
+ <li><a href="#help">Help</a>
+ <ul>
+ <!-- Sequence: 10 -->
+ <!-- Home/Default -->
+ <li><a href="/app/template/ReportIssue.vm">Report a Problem</a></li>
+ <li><a href="http://wiki.xnat.org/display/XNAT16/Home" target="_blank">Documentation</a></li>
+ </ul>
+ </li>
+ </ul>
+
+ <!-- search script -->
+ <script type="text/javascript">
+ <!--
+ function DefaultEnterKey(e, button) {
+ var keynum, keychar, numcheck;
+
+ if (window.event) // IE
+ {
+ keynum = e.keyCode;
+ if (keynum == 13) {
+ submitQuickSearch();
+ return true;
+ }
+ }
+ else if (e) // Netscape/Firefox/Opera
+ {
+ keynum = e.which;
+ if (keynum == 13) {
+ submitQuickSearch();
+ return false;
+ }
+ }
+ return true;
+ }
+
+ function submitQuickSearch() {
+ concealContent();
+ if (document.getElementById('quickSearchForm').value != "")
+ document.getElementById('quickSearchForm').submit();
+ }
+
+ //-->
+ </script>
+ <!-- end search script -->
+
+ <style type="text/css">
+ #quickSearchForm .chosen-results {
+ max-height: 500px;
+ }
+
+ #quickSearchForm .chosen-results li {
+ padding-right: 20px;
+ white-space: nowrap;
+ }
+
+ #quickSearchForm .chosen-container .chosen-drop {
+ width: auto;
+ min-width: 180px;
+ max-width: 360px;
+ }
+
+ #quickSearchForm .chosen-container .chosen-drop .divider {
+ padding: 0;
+ overflow: hidden;
+ }
+ </style>
+
+ <form id="quickSearchForm" method="post" action="/app/action/QuickSearchAction">
+ <select id="stored-searches" data-placeholder="Stored Searches">
+ <option></option>
+ <optgroup>
+ <option value="/app/template/XDATScreen_search_wizard1.vm">Advanced Search…</option>
+ </optgroup>
+ <optgroup class="stored-search-list">
+ <option disabled>(no stored searches)</option>
+ <!-- stored searches will show up here -->
+ </optgroup>
+ </select>
+ <input id="searchValue" class="clean" name="searchValue" type="text" maxlength="40" size="20" value=""/>
+ <button type="button" id="search_btn" class="btn2" onclick="submitQuickSearch();">Go</button>
+
+ <script>
+ $('#searchValue').each(function () {
+ this.value = this.value || 'search';
+ $(this).focus(function () {
+ $(this).removeClass('clean');
+ if (!this.value || this.value === 'search') {
+ this.value = '';
+ }
+ })
+ });
+ $('#stored-searches').on('change', function () {
+ if (this.value) {
+ window.location.href = this.value;
+ }
+ }).chosen({
+ width: '150px',
+ disable_search_threshold: 9,
+ inherit_select_classes: true,
+ placeholder_text_single: 'Stored Searches',
+ search_contains: true
+ });
+ </script>
+ </form>
+
+
+ </div>
+ <!-- /main_nav -->
+
+ <!-- main_nav interactions -->
+ <script type="text/javascript">
+
+ (function () {
+
+ // cache it
+ var main_nav$ = jq('#main_nav > ul');
+
+ var body$ = jq('body');
+
+ var cover_up_count = 1;
+
+ function coverApplet(el$) {
+ var cover_up_id = 'cover_up' + cover_up_count++;
+ var jqObjPos = el$.offset(),
+ jqObjLeft = jqObjPos.left,
+ jqObjTop = jqObjPos.top,
+ jqObjMarginTop = el$.css('margin-top'),
+ jqObjWidth = el$.outerWidth() + 4,
+ jqObjHeight = el$.outerHeight() + 2;
+
+ el$.before('<iframe id="' + cover_up_id + '" class="applet_cover_up" src="about:blank" width="' + jqObjWidth + '" height="' + jqObjHeight + '"></iframe>');
+
+ jq('#' + cover_up_id).css({
+ display: 'block',
+ position: 'fixed',
+ width: jqObjWidth,
+ height: jqObjHeight,
+ marginTop: jqObjMarginTop,
+ left: jqObjLeft,
+ top: jqObjTop,
+ background: 'transparent',
+ border: 'none',
+ outline: 'none'
+ });
+ }
+
+ function unCoverApplets(el$) {
+ el$.prev('iframe.applet_cover_up').detach();
+ }
+
+ function fadeInNav(el$) {
+ el$.find('> ul').show().addClass('open');
+ }
+
+ function fadeOutNav(el$) {
+ el$.find('> ul').hide().removeClass('open');
+ }
+
+ // give menus with submenus a class of 'more'
+ main_nav$.find('li ul, li li ul').closest('li').addClass('more');
+ main_nav$.find('li li ul').addClass('subnav');
+
+ // no fancy fades on hover
+ main_nav$.find('li.more').on('mouseover',
+ function () {
+ var li$ = $(this);
+ fadeInNav(li$);
+ li$.find('ul.subnav').each(function () {
+ var sub$ = $(this);
+ var offsetL = sub$.closest('ul').outerWidth();
+ sub$.css({'left': offsetL + -25})
+ });
+ if (body$.hasClass('applet')) {
+ coverApplet(li$.find('> ul'));
+ }
+ }
+ ).on('mouseout',
+ function () {
+ var li$ = $(this);
+ fadeOutNav(li$);
+ if (body$.hasClass('applet')) {
+ unCoverApplets(li$.find('> ul'));
+ }
+ }
+ );
+
+ // clicking the "Logout" link sets the warning bar cookie to 'OPEN' so it's available if needed on next login
+ jq('#logout_user').click(function () {
+ Cookies.set('WARNING_BAR', 'OPEN', {path: '/'});
+ Cookies.set('NOTIFICATION_MESSAGE', 'OPEN', {path: '/'});
+ });
+
+ })();
+ </script>
+ <!-- end main_nav interactions -->
+
+ <div id="header" class="main_header">
+ <div class="pad">
+
+ <a id="header_logo" href="/app/template/Index.vm" style="display:none;">
+ <img class="logo_img" src="/images/logo.png" style="border:none;"> </a>
+
+ </div>
+ </div> <!-- /header -->
+
+
+ <script type="text/javascript">
+
+ (function () {
+
+ var header_logo$ = $('#header_logo');
+
+ // adjust height of header if logo is taller than 65px
+ var hdr_logo_height = header_logo$.height();
+ if (hdr_logo_height > 65) {
+ jq('.main_header').height(hdr_logo_height + 10);
+ }
+
+ // adjust width of main nav if logo is wider than 175px
+ var hdr_logo_width = header_logo$.width();
+ if (hdr_logo_width > 175) {
+ jq('#main_nav').width(932 - hdr_logo_width - 20);
+ }
+
+ //
+ //var recent_proj_height = jq('#min_projects_list > div').height();
+ var recent_proj_height = 67;
+ //jq('#min_projects_list, #min_expt_list').height(recent_proj_height * 5).css({'min-width':349,'overflow-y':'scroll'});
+
+ })();
+
+ logged_in = true;
+
+ // initialize the advanced search method toggler
+ XNAT.app.searchMethodToggler = function (_parent) {
+
+ _parent = $$(_parent || 'body');
+
+ var INPUTS = 'input, select, textarea, :input',
+ SEARCH_METHOD_CKBOXES = 'input.search-method',
+ __searchGroups = _parent.find('div.search-group'),
+ __searchMethodInputs = _parent.find(SEARCH_METHOD_CKBOXES);
+
+ // disable 'by-id' search groups by default
+ __searchGroups.filter('.by-id').addClass('disabled').find(INPUTS).not(SEARCH_METHOD_CKBOXES).changeVal('').prop('disabled', true).addClass('disabled');
+
+ // enable 'by-criteria' search groups by default
+ __searchGroups.filter('.by-criteria').removeClass('disabled').find(INPUTS).prop('disabled', false).removeClass('disabled');
+
+ // check 'by-criteria' checkboxes
+ __searchMethodInputs.filter('.by-criteria').prop('checked', true);
+
+ // don't add multiple click handlers
+ __searchMethodInputs.off('click');
+
+ // toggle the search groups
+ __searchMethodInputs.on('click', function () {
+
+ var method = this.value,
+ isChecked = this.checked;
+
+ __searchGroups.addClass('disabled').find(INPUTS).not(SEARCH_METHOD_CKBOXES).changeVal('').prop('disabled', true).addClass('disabled');
+
+ __searchGroups.filter('.' + method).removeClass('disabled').find(INPUTS).prop('disabled', false).removeClass('disabled');
+
+ // update the radio buttons/checkboxes
+ __searchMethodInputs.prop('checked', false);
+ __searchMethodInputs.filter('.' + method).prop('checked', true);
+ chosenUpdate();
+ });
+ };
+
+ </script>
+
+ <script src="/scripts/timeLeft.js"></script>
+
+ <div id="tp_fm"></div>
+
+ <!-- END: xnat-templates/navigations/DefaultTop.vm -->
+
+ <!-- /xnat-templates/navigations/DefaultLeft.vm -->
+
+ <div id="l_tv" style="display:none;"></div>
+
+ <script type="text/javascript">
+ //build element_array
+ var lTV = new LeftBarTreeView({treeview: "l_tv"});
+
+ lTV.loadNodeData = function (node, fnLoadComplete) {
+ var tabReqObject = node.data;
+ tabReqObject.label = node.label;
+ tabReqObject.node = node;
+ if (tabReqObject.URL != undefined) {
+ window.location = serverRoot + "/app/template/Search.vm/node/" + tabReqObject.ID;
+ }
+ else {
+ if (tabReqObject.ID != undefined && tabReqObject.ID == "ss") {
+ var callback = {
+ cache: false, // Turn off caching for IE
+ success: function (oResponse) {
+ var oResults = eval("(" + oResponse.responseText + ")");
+ if ((oResults.ResultSet.Result) && (oResults.ResultSet.Result.length)) {
+ for (var ssC = 0; ssC < oResults.ResultSet.Result.length; ssC++) {
+ var cpNode = new YAHOO.widget.TextNode({
+ label: oResults.ResultSet.Result[ssC].brief_description,
+ ID: "ss." + oResults.ResultSet.Result[ssC].id,
+ SS_ID: oResults.ResultSet.Result[ssC].id,
+ URL: serverRoot + '/REST/search/saved/' + oResults.ResultSet.Result[ssC].id + '',
+ TITLE: oResults.ResultSet.Result[ssC].description
+ }, oResponse.argument.node, false);
+ }
+ }
+ oResponse.argument.fnLoadComplete();
+ },
+ failure: function (oResponse) {
+ oResponse.argument.fnLoadComplete();
+ },
+ argument: {"node": node, "fnLoadComplete": fnLoadComplete}
+ };
+
+ //YAHOO.util.Connect.asyncRequest('GET',this.obj.URL,this.initCallback,null,this);
+ YAHOO.util.Connect.asyncRequest('GET', serverRoot + '/REST/search/saved?XNAT_CSRF=' + window.csrfToken + '&format=json&stamp=' + (new Date()).getTime(), callback, null);
+ }
+ else {
+ fnLoadComplete();
+ }
+ }
+ }
+
+ lTV.init();
+
+ </script>
+ <!-- end /xnat-templates/navigations/DefaultLeft.vm -->
+
+ <div id="breadcrumbs"></div>
+ <script src="/scripts/xnat/ui/breadcrumbs.js"></script>
+ <script language="javascript">
+
+ window.isProjectPage = (XNAT.data.context.xsiType === 'xnat:projectData');
+
+ // wrap it up to keep things
+ // out of global scope
+ (function () {
+
+ var crumbs = [];
+
+
+ XNAT.ui.breadcrumbs.render('#breadcrumbs', crumbs);
+
+
+ })();
+
+ </script>
+
+ <div id="layout_content2" style="display:none;">Loading...</div>
+ <div id="layout_content">
+ <!--BEGIN SCREEN CONTENT -->
+
+ <jsp:doBody scope="page"/>
+
+ <!-- END SCREEN CONTENT -->
+ </div>
+
+ <div id="mylogger"></div>
+
+
+ <!-- path: xnat-templates/navigations/htmlClose -->
+</div><!-- /page_wrapper -->
+
+<div id="xnat_power">
+ <a target="_blank" href="http://www.xnat.org/" style=""><img src="/images/xnat_power_small.png"></a>
+</div>
+
+<script type="text/javascript">
+
+ loadjs(scriptUrl('xnat/event.js'), function () {
+
+ // shift-click the header or footer XNAT logo to ENABLE debug mode
+ // alt-shift-click to DISABLE debug mode
+ XNAT.event.click('#header_logo, #xnat_power > a')
+ .shiftKey(function (e) {
+ e.preventDefault();
+ window.location.hash = 'debug=on'
+ window.location.reload();
+ })
+ .altShift(function (e) {
+ e.preventDefault();
+ window.location.hash = 'debug=off'
+ window.location.reload();
+ });
+
+ })
+
+</script>
+<script type="text/javascript" src="/scripts/footer.js"></script>
+</body>
+</html>
diff --git a/src/main/webapp/WEB-INF/views/spawner/element.jsp b/src/main/webapp/WEB-INF/views/spawner/element.jsp
new file mode 100644
index 00000000..e69de29b
diff --git a/src/main/webapp/WEB-INF/views/spawner/elements.jsp b/src/main/webapp/WEB-INF/views/spawner/elements.jsp
new file mode 100644
index 00000000..ed05c3b0
--- /dev/null
+++ b/src/main/webapp/WEB-INF/views/spawner/elements.jsp
@@ -0,0 +1,257 @@
+<!-- BEGIN views/spawner/elements.jsp -->
+<%@ page contentType="text/html" pageEncoding="UTF-8" %>
+<%@ taglib prefix="sp" tagdir="/WEB-INF/tags/spawner" %>
+<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
+<jsp:useBean id="elements" scope="request" type="java.util.List"/>
+<jsp:useBean id="element" scope="request" type="org.nrg.xnat.spawner.entities.SpawnerElement"/>
+
+<sp:layout title="Spawner Elements">
+ <h3 style="margin:0 0 15px 0;">Spawner Elements</h3>
+
+ <div style="margin:15px 0;max-width:696px;min-width:400px;">
+ The Spawner is XNAT's system for managing dynamically configurable user interface elements.
+ </div>
+
+ <div class="yui-skin-sam">
+
+ <style type="text/css" scoped="scoped">
+ #automation-events-scripts .yui-content > div {
+ padding: 2px;
+ }
+
+ td.edit:hover {
+ cursor: pointer
+ }
+
+ td.edit:hover a,
+ td.actions a:hover {
+ text-decoration: underline
+ }
+
+ td.edit a,
+ td.actions a {
+ display: inline-block;
+ padding: 2px 8px;
+ }
+
+ table.edit-script {
+ margin-bottom: -4px;
+ }
+
+ table.edit-script td {
+ padding: 4px 2px;
+ vertical-align: baseline;
+ }
+ </style>
+
+ <script type="text/javascript" src="/scripts/xnat/app/siteEventsManager.js"></script>
+ <script type="text/javascript" src="scripts/uploaders/AutomationBasedUploader.js"></script>
+
+ <div id="addEventHandler" class="html-template">
+ <table>
+ <tr>
+ <td><label for="select_event" class="required"><strong>Event:</strong><i>*</i></label></td>
+ <td><select id="select_event" name="event" class="event"></select></td>
+ </tr>
+ <tr>
+ <td><label for="select_scriptId" class="required"><strong>Script ID:</strong><i>*</i></label></td>
+ <td><select id="select_scriptId" name="scriptId" class="scriptId"></select></td>
+ </tr>
+ <tr>
+ <td><label for="description"><strong>Description:</strong></label></td>
+ <td><input id="description" name="description" class="description" type="text" size="40"></td>
+ </tr>
+ </table>
+ </div>
+
+ <!-- SITE EVENTS TABLE ROW TEMPLATE -->
+ <table id="event-row-template" class="html-template">
+ <tbody>
+ <tr class="highlight events-list">
+ <td class="site-event-id">
+ </td>
+ <td class="site-event-label">
+ </td>
+ <td class="workflow-label"></td>
+ <td class="actions" style="text-align:center;white-space:nowrap;">
+ </td>
+ </tr>
+ </tbody>
+ </table>
+
+ <table id="script-row-template" class="html-template">
+ <tbody>
+ <tr class="highlight script-list" data-script-id="__SCRIPT_ID__">
+ <td class="edit">
+ </td>
+ <td class="edit" data-action="editScript"></td>
+ <td class="actions" style="text-align:center;white-space:nowrap;">
+ </td>
+ </tr>
+ </tbody>
+ </table>
+
+ <div class="yui-content">
+
+ <table id="elements-table" class="xnat-table" style="width: 100%;">
+
+ <thead>
+ <tr><th width="40%">Element</th>
+ <th width="40%">Description</th>
+ <th width="20%"> </th>
+ </tr></thead>
+
+ <tbody>
+ <c:forEach var="element" items="${elements}">
+ <tr class="highlight events-list">
+ <td class="site-event-id">
+ ${element.label}
+ </td>
+ <td class="site-event-label">
+ ${element.description}
+ </td>
+ <td class="actions" style="text-align:center;white-space:nowrap;">
+ <a href="#!" class="edit-event" data-action="editEvent"
+ title="edit existing event">edit</a>
+ <a href="#!" class="delete-event" data-action="deleteEvent"
+ title="delete existing event">delete</a>
+ </td>
+ </tr>
+ </c:forEach>
+ </tbody>
+
+ </table>
+
+ </div>
+
+ <script type="text/javascript">
+
+ // YUI tab simulator using jQuery for event handling for '.bogus-tabs'
+ // using 'on' to handle any tabs that may be added dynamically
+ jq('.yui-navset.bogus-tabs').each(function () {
+
+ var __navset = jq(this),
+ TABS = '> ul.yui-nav > li',
+ CONTENTS = '> .yui-content > div',
+ selected = null;
+
+ __navset.on('click', TABS + '> a', function (e) {
+
+ e.preventDefault();
+
+ var __link = jq(this),
+ __tab = __link.closest('li');
+
+ selected = __link.attr('href'); // safer to use jQuery to get 'href' value
+
+ __navset.find(TABS).removeClass('selected');
+ __tab.addClass('selected');
+
+ __navset.find(CONTENTS).addClass('yui-hidden');
+ __navset.find(selected).removeClass('yui-hidden');
+
+ });
+
+ });
+
+ </script>
+
+ <!-- SITE EVENTS DIALOG TEMPLATE -->
+ <div id="site-events-template" class="html-template">
+ <p>Select a Workflow or enter a new Event name to define an Event to use with project and site Event
+ Handlers:</p>
+ <table>
+ <tr>
+ <td><label for="workflow-event-id-menu" class="required"><strong>Workflow:</strong><i>*</i></label>
+ </td>
+ <td>
+
+ <div id="workflow-event-id-container">
+ ## workflow events menu
+ </div>
+ ## <select id="workflow-event-id-menu" name="event_id" class="event_id active">
+ ##
+ <option data-label="__WORKFLOW_EVENT_LABEL__" data-id="__WORKFLOW_EVENT_ID__"
+ value="__WORKFLOW_EVENT_ID__">__WORKFLOW_EVENT_LABEL__
+ </option>
+ ## </select>
+
+ </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>
+ <div id="custom-event-id" style="padding:10px 0;">
+ <input type="checkbox" id="custom-event-checkbox">
+ <label for="custom-event-checkbox">Or enter a custom Event id:</label>
+ <br>
+ <input type="text" id="custom-event-input" class="event_id"
+ placeholder="(enter custom Event id)" disabled>
+ </div>
+ </td>
+ </tr>
+ ##
+ <tr>
+ ##
+ <td><label for="scriptId" class="required"><strong>Script ID:</strong><i>*</i></label></td>
+ ##
+ <td><select id="scriptId" name="scriptId" class="scriptId"></select></td>
+ ##
+ </tr>
+ <tr>
+ <td><label for="events-event-label"><strong>Label:</strong></label></td>
+ <td>
+ <input id="events-event-label" name="event_label" class="event_label" type="text" size="40">
+ </td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>
+ <small>Label not required. If no label is entered, it will be the same as the ID.</small>
+ </td>
+ </tr>
+ </table>
+ </div>
+
+ <!-- SCRIPT EDITOR TEMPLATE -->
+ <div id="script-editor-template" class="html-template">
+ <input type="hidden" name="id" class="id" value="">
+ <input type="hidden" name="scriptId" class="scriptId" value="">
+ <input type="hidden" name="language" class="language" value="">
+ <input type="hidden" name="languageVersion" class="languageVersion" value="">
+ <input type="hidden" name="timestamp" class="timestamp" value="">
+ <table class="edit-script" border="0" cellspacing="0">
+ <tr>
+ <td><b>Script ID: </b> </td>
+ <td>
+ <b class="script-id-text"></b>
+ <input type="text" name="script-id-input" class="script-id-input" size="30" value="">
+ </td>
+ </tr>
+ <tr>
+ <td><b>Description: </b> </td>
+ <td><input type="text" name="script-description" class="script-description" size="80" value=""></td>
+ </tr>
+ <tr>
+ <td><b>Script Version: </b> </td>
+ <td><select id="script-version" class="script-version">
+ <option value="!">Select a Version</option>
+ </select></td>
+ </tr>
+ </table>
+ <br>
+ <div class="editor-wrapper" style="width:840px;height:482px;position:relative;">
+ <!-- the '.editor-content' div gets replaced when the script content is loaded -->
+ <div class="editor-content"
+ style="position:absolute;top:0;right:0;bottom:0;left:0;border:1px solid #ccc;"></div>
+ </div>
+ </div><!-- /#script-editor-template -->
+
+ <script type="text/javascript" src="/scripts/lib/ace/ace.js"></script>
+ <script type="text/javascript" src="/scripts/xnat/app/automation.js"></script>
+ <script type="text/javascript" src="/scripts/xnat/app/scriptEditor.js"></script>
+
+ </div>
+
+</sp:layout>
+<!-- END views/spawner/elements.jsp -->
\ No newline at end of file
--
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