grnsight 4.0.0 → 6.0.0

package/_gh_pages/assets/js/ga-report.js

@@ -1,19 +1,19 @@
 $(function () {
     var getCount = function (path, callback) {
-            $.getJSON("http://grnsight.cs.lmu.edu/server/ga?path=" + path).done(callback);
-        },
+        $.getJSON("https://grnsight.cs.lmu.edu/server/ga?path=" + path).done(callback);
+    };
 
-        setReportResult = function (count) {
-            $(".ga-report").text(count);            
-        },
+    var setReportResult = function (count) {
+        $(".ga-report").text(count);
+    };
 
-        getUploadCount = function () {
-            getCount("upload", function (uploadCount) {
-                $(".ga-upload").text(uploadCount);
-            });
-        },
+    var getUploadCount = function () {
+        getCount("upload", function (uploadCount) {
+            $(".ga-upload").text(uploadCount);
+        });
+    };
 
-        pathTail = location.pathname.split("/").pop();
+    var pathTail = location.pathname.split("/").pop();
 
     getCount(pathTail, function (pathCount) {
         if (pathTail === "") {

package/_gh_pages/assets/js/iframeResizer.min.js

@@ -0,0 +1,9 @@
+/*! iFrame Resizer (iframeSizer.min.js ) - v4.1.1 - 2019-04-10
+ *  Desc: Force cross domain iframes to size to content.
+ *  Requires: iframeResizer.contentWindow.min.js to be loaded into the target frame.
+ *  Copyright: (c) 2019 David J. Bradshaw - dave@bradshaw.net
+ *  License: MIT
+ */
+
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+//# sourceMappingURL=iframeResizer.map

package/_gh_pages/assets/js/main.js

@@ -2,8 +2,8 @@ $(function () {
 
     var LEFT_WINDOW_BOUNDARY = 1;
     var SCROLL_START_POINT = 140;
-    var LOGO_DEFAULT = '/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg';
-    var LOGO_HOVER = '/GRNsight/assets/images/GRNsight_logo_20140710_rollover_resized.jpg';
+    var LOGO_DEFAULT = "/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg";
+    var LOGO_HOVER = "/GRNsight/assets/images/GRNsight_logo_20140710_rollover_resized.jpg";
 
     var PRIVACY_COOKIE = "_grnsight_privacy_";
     var checkForPrivacyCookie = function () {
@@ -42,84 +42,84 @@ $(function () {
     };
 
     var changeImageOnHover = function (contentID, imageSrcDefault, imageSrcOnHover) {
-        $(contentID).on('mouseenter', function () {
-            $(contentID).attr('src', imageSrcOnHover)
-        }).on('mouseleave', function () {
-            $(contentID).attr('src', imageSrcDefault)
-        })
+        $(contentID).on("mouseenter", function () {
+            $(contentID).attr("src", imageSrcOnHover);
+        }).on("mouseleave", function () {
+            $(contentID).attr("src", imageSrcDefault);
+        });
+    };
+
+    var detachSidebar = function (sidebarID) {
+        $(sidebarID).attr("class", "affix-top");
+    };
+
+    var attachSidebar = function (sidebarID) {
+        $(sidebarID).attr("class", "affix");
     };
 
     var disableSidebarHorizontalMovement = function (sidebarID) {
         $(window).scroll(function() {
-            var userHasScrolledRight = $(window).scrollLeft() >= LEFT_WINDOW_BOUNDARY,
-            sidebarShouldScroll = $(window).scrollTop() > SCROLL_START_POINT,
-            sidebarIsAttached = ($(sidebarID).attr('class')) === 'affix' ? true : false;
+            var userHasScrolledRight = $(window).scrollLeft() >= LEFT_WINDOW_BOUNDARY;
+            var sidebarShouldScroll = $(window).scrollTop() > SCROLL_START_POINT;
+            var sidebarIsAttached = ($(sidebarID).attr("class")) === "affix" ? true : false;
             if ((userHasScrolledRight && sidebarShouldScroll) || (!sidebarShouldScroll && sidebarIsAttached)) {
                 detachSidebar(sidebarID);
-            } else if(sidebarShouldScroll && !sidebarIsAttached) {
+            } else if (sidebarShouldScroll && !sidebarIsAttached) {
                 attachSidebar(sidebarID);
-            } 
+            }
         });
     };
 
-    var detachSidebar = function (sidebarID) {
-        $(sidebarID).attr('class', 'affix-top');
-    };
-
-    var attachSidebar = function (sidebarID) {
-        $(sidebarID).attr('class', 'affix');
-    };
-
     var openCollapsedHashedElements = function () {
         // Open a hashed element if it is collapsed.  This is a little trickier than it sounds,
         // because then we also have to open any parents that are also collapsed.
         if (location.hash) {
             var $elementToOpen = $(location.hash);
-            if ($elementToOpen.is('.collapse:not(.in)')) {
-                $elementToOpen.parents('.collapse:not(.in)').collapse('show');
-                $elementToOpen.collapse('show');
+            if ($elementToOpen.is(".collapse:not(.in)")) {
+                $elementToOpen.parents(".collapse:not(.in)").collapse("show");
+                $elementToOpen.collapse("show");
             }
         }
     };
 
-    var setupDocumentationPanels = function () {
-        var documentationPanelInformation = [ [ '.showSection2', '#section2Content', '#section2' ],
-                                              [ '.showSection3', '#section3Content', '#section3' ] ];
-        documentationPanelInformation.forEach(function (panelInfo) {
-            configurePanelBehavior.apply(null, panelInfo);
-        });
+    var focusWindowOn = function (location) {
+        window.location.href = location;
     };
 
-    var configurePanelBehavior = function (linkToPanel, panelID, targetHref) {
-        $(panelID).on('shown.bs.collapse', function () {
-            focusWindowOn(targetHref);
-        });
-        changePageFocusEvenIfPanelsOpen(linkToPanel, panelID, targetHref);
+    var openPanel = function (panelID) {
+        $(panelID).collapse("show");
     };
 
     var changePageFocusEvenIfPanelsOpen = function (linkToPanel, panelID, targetHref) {
-        $(linkToPanel).on('click', function () {
+        $(linkToPanel).on("click", function () {
             openPanel(panelID);
 
-            var panelWasClosed = $(panelID).attr('class') === 'panel-collapse collapse in';
+            var panelWasClosed = $(panelID).attr("class") === "panel-collapse collapse in";
             if (panelWasClosed) {
                 focusWindowOn(targetHref);
-            };
+            }
         });
     };
 
-    var focusWindowOn = function (location) {
-        window.location.href = location;
+    var configurePanelBehavior = function (linkToPanel, panelID, targetHref) {
+        $(panelID).on("shown.bs.collapse", function () {
+            focusWindowOn(targetHref);
+        });
+        changePageFocusEvenIfPanelsOpen(linkToPanel, panelID, targetHref);
     };
 
-    var openPanel = function (panelID) {
-        $(panelID).collapse('show');
+    var setupDocumentationPanels = function () {
+        var documentationPanelInformation = [ [ ".showSection2", "#section2Content", "#section2" ],
+                                              [ ".showSection3", "#section3Content", "#section3" ] ];
+        documentationPanelInformation.forEach(function (panelInfo) {
+            configurePanelBehavior.apply(null, panelInfo);
+        });
     };
 
     var initializePage = function () {
         checkForPrivacyCookie();
-        changeImageOnHover('#GRNsightLogo', LOGO_DEFAULT, LOGO_HOVER);
-        disableSidebarHorizontalMovement('#stickyBar');
+        changeImageOnHover("#GRNsightLogo", LOGO_DEFAULT, LOGO_HOVER);
+        disableSidebarHorizontalMovement("#stickyBar");
         openCollapsedHashedElements();
 
         var pageIsDocumentationPage = (location.pathname === "/GRNsight/documentation.html");

package/_gh_pages/beta.html

@@ -3,27 +3,23 @@
 
     <head>
         <title>GRNsight - Beta</title>
-        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/bootstrap.min.css">
+        <link rel="shortcut icon" type="image/x-icon" href="favicon.ico">
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous">
         <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/main.css">
         <meta charset="utf-8">
-        <!-- Begin Jekyll SEO tag v2.0.0 -->
+        <!-- Begin Jekyll SEO tag v2.6.1 -->
+<meta name="generator" content="Jekyll v3.9.0" />
 <meta property="og:title" content="Beta" />
-<meta name="description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<meta property="og:description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<link rel="canonical" href="http://dondi.github.io/GRNsight/beta.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/beta.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="Beta version of GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<meta property="og:description" content="Beta version of GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/beta.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/beta.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
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-    "headline": "Beta",
-    "description": "GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.",
-    "logo": "http://dondi.github.io/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg",
-    "url": "http://dondi.github.io/GRNsight/beta.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/beta.html","description":"Beta version of GRNsight, an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"Beta","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
+
     </head>
 
 
@@ -38,7 +34,7 @@
             </div>
             <p id="title"><a href="/GRNsight">GRNsight</a></p>
             <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
-            <div class="alert alert-success hidden" id="cookie-notice" role="alert">
+            <div class="alert alert-success d-none" id="cookie-notice" role="alert">
                 <div>This site uses Google Analytics to count pageviews and file uploads to demonstrate usage of our software to interested parties such as our employers and funding agencies. Information about your use of this site is shared with Google. By using this site, you agree to its use of cookies.</div>
                 <button class="cookie-action" data-dismiss="alert" aria-label="Got It">
                     <strong>Got It</strong>
@@ -68,19 +64,19 @@
 
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 9/6/15
+                    Last modified: 10/05/2020
                 </p>
             </div>
+
         </div>
 
         <div id="mainContent">
-            <p id="pageTitle">Beta <span id="version">v1.13</span></p>
-            <div id="pageContent">
+            <p id="pageTitle">Beta <span id="version">v4.0.22</span></p>
+            <div id="graphPageContent">
                 <p><span style="font-weight:bold">Disclaimer: </span>This is the beta version of GRNsight for live testing of new functionality. For the most stable version, please go to the <a href="/GRNsight/">GRNsight home page</a>.</p>
-                <iframe class="embedded-demo" src="http://grnsight.cs.lmu.edu/beta/client"></iframe>
+                <iframe class="embedded-demo" src="https://grnsight.cs.lmu.edu/beta/client"></iframe>
             </div>
 
-
             <div id="footer">
                 <hr id="separate">
                 <ul id="footerNav">
@@ -119,7 +115,7 @@
             </div>
         </div>
 
-        <script>
+          <script>
             (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
                 (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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@@ -128,10 +124,19 @@
             ga("create", "UA-54882218-1", "auto");
             ga("send", "pageview");
         </script>
-        <script src="https://code.jquery.com/jquery.js"></script>
-        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
+        <script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
+        <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
         <script src="/GRNsight/assets/js/main.js"></script>
         <script src="/GRNsight/assets/js/ga-report.js"></script>
+    
+        <!-- Placeholder for whatever the final iframe management solution will be. -->
+    
+    
+    
+        <script src="/GRNsight/assets/js/iframeResizer.min.js"></script>
+        <script src="https://grnsight.cs.lmu.edu/beta/client/js/iframe-coordination.js"></script>
+    
 
 
     </body>

package/_gh_pages/contact.html

@@ -3,27 +3,23 @@
 
     <head>
         <title>GRNsight - Contact</title>
-        <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/bootstrap.min.css">
+        <link rel="shortcut icon" type="image/x-icon" href="favicon.ico">
+        <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" integrity="sha384-JcKb8q3iqJ61gNV9KGb8thSsNjpSL0n8PARn9HuZOnIxN0hoP+VmmDGMN5t9UJ0Z" crossorigin="anonymous">
         <link rel="stylesheet" type="text/css" href="/GRNsight/assets/css/main.css">
         <meta charset="utf-8">
-        <!-- Begin Jekyll SEO tag v2.0.0 -->
+        <!-- Begin Jekyll SEO tag v2.6.1 -->
+<meta name="generator" content="Jekyll v3.9.0" />
 <meta property="og:title" content="Contact" />
-<meta name="description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<meta property="og:description" content="GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks." />
-<link rel="canonical" href="http://dondi.github.io/GRNsight/contact.html" />
-<meta property="og:url" content="http://dondi.github.io/GRNsight/contact.html" />
+<meta property="og:locale" content="en_US" />
+<meta name="description" content="Contact information for the Principal Investigators of the GRNsight gene regulatory network visualization web application." />
+<meta property="og:description" content="Contact information for the Principal Investigators of the GRNsight gene regulatory network visualization web application." />
+<link rel="canonical" href="http://localhost:3001/GRNsight/contact.html" />
+<meta property="og:url" content="http://localhost:3001/GRNsight/contact.html" />
 <meta property="og:site_name" content="GRNsight" />
 <script type="application/ld+json">
-  {
-    "@context": "http://schema.org",
-    "@type": "WebPage",
-    "headline": "Contact",
-    "description": "GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks.",
-    "logo": "http://dondi.github.io/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg",
-    "url": "http://dondi.github.io/GRNsight/contact.html"
-  }
-</script>
+{"@type":"WebPage","url":"http://localhost:3001/GRNsight/contact.html","description":"Contact information for the Principal Investigators of the GRNsight gene regulatory network visualization web application.","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:3001/GRNsight/assets/images/GRNsight_logo_20140710_main_resized.jpg"}},"headline":"Contact","@context":"https://schema.org"}</script>
 <!-- End Jekyll SEO tag -->
+
     </head>
 
 
@@ -38,7 +34,7 @@
             </div>
             <p id="title"><a href="/GRNsight">GRNsight</a></p>
             <p id="subtext">Web app and service for visualizing models of gene regulatory networks.</p>
-            <div class="alert alert-success hidden" id="cookie-notice" role="alert">
+            <div class="alert alert-success d-none" id="cookie-notice" role="alert">
                 <div>This site uses Google Analytics to count pageviews and file uploads to demonstrate usage of our software to interested parties such as our employers and funding agencies. Information about your use of this site is shared with Google. By using this site, you agree to its use of cookies.</div>
                 <button class="cookie-action" data-dismiss="alert" aria-label="Got It">
                     <strong>Got It</strong>
@@ -68,27 +64,28 @@
 
                 </ul>
                 <p id="modText" class="modNav">
-                    Last modified: 12/30/15
+                    Last modified: 6/1/18
                 </p>
             </div>
+
         </div>
 
         <div id="mainContent">
             <p id="pageTitle">Contact</p>
             <div id="pageContent">
                 <p style="padding-left:30px">
-                    To request support or features or report bugs, please go to <a href="https://github.com/dondi/GRNsight" target="_blank">GRNsight @ GitHub</a>.
+                    To request support or features or report bugs, please submit an <a href="https://github.com/dondi/GRNsight/issues">issue</a> to <a href="https://github.com/dondi/GRNsight" target="_blank">GRNsight @ GitHub</a> (requires free GitHub account).
                     <br><br>
-                    For all other correspondence, please contact:
+                    For all other correspondence, please contact the Principal Investigators:
                 </p>
                 <p class="name">Kam D. Dahlquist, Ph.D.</p>
                 <p class="personInfo">
-                    Associate Professor <br>
+                    Professor <br>
                     Department of Biology (Life Sciences Building 289) <br>
-                    <a href="http://myweb.lmu.edu/kdahlqui/">http://myweb.lmu.edu/kdahlqui</a> <br><br>
+                    <a href="http://kdahlquist.github.io/DahlquistLab/">http://kdahlquist.github.io/DahlquistLab/</a> <br><br>
                     Loyola Marymount University <br>
                     1 LMU Drive, MS 8888 <br>
-                    Los Angeles, CA 90045-2659 <br>
+                    Los Angeles, CA 90045-2659 USA<br>
                     Tel: 310-338-7697 <br>
                     Fax: 310-338-5317 <br>
                     <a href="mailto:kdahlquist@lmu.edu">kdahlquist@lmu.edu</a>
@@ -96,28 +93,27 @@
                 <p class="name">John David N. Dionisio, Ph.D.</p>
                 <p class="personInfo">Professor <br>
                     Department of Electrical Engineering &amp; Computer Science (Doolan 106) <br>
-                    <a href="http://myweb.lmu.edu/dondi">http://myweb.lmu.edu/dondi</a> <br><br>
+                    <a href="http://dondi.lmu.build/">http://dondi.lmu.build/</a> <br><br>
                     Loyola Marymount University <br>
                     1 LMU Drive, MS 8145 <br>
-                    Los Angeles, CA 90045-2659 <br>
+                    Los Angeles, CA 90045-2659 USA<br>
                     Tel: 310-338-5782 <br>
                     <a href="mailto:dondi@lmu.edu">dondi@lmu.edu</a>
                 </p> <br>
                 <p class="name">Ben G. Fitzpatrick, Ph.D.</p>
                 <p class="personInfo">
                     Professor <br>
-                    Department of Mathematics (UH 2726) <br>
-                    <a href="http://myweb.lmu.edu/bfitzpatrick">http://myweb.lmu.edu/bfitzpatrick</a> <br><br>
+                    Department of Mathematics (UH 2726) <br><br>
                     Loyola Marymount University <br>
                     1 LMU Drive <br>
-                    Los Angeles, CA 90045-2659 <br>
+                    Los Angeles, CA 90045-2659 USA<br>
                     Tel: 310-338-7892 <br>
                     <a href="mailto:bfitzpatrick@lmu.edu">bfitzpatrick@lmu.edu</a>
                 </p> <br>
                 <p class="name">Loyola Marymount University</p>
                 <p class="personInfo">
                     1 LMU Drive <br>
-                    Los Angeles, CA 90045-2659 <br><br>
+                    Los Angeles, CA 90045-2659 USA<br><br>
                     <a href="http://www.lmu.edu/resources/campusmaps/">Loyola Marymount University Campus Maps</a>
                 </p>
             </div>
@@ -158,7 +154,7 @@
             </div>
         </div>
 
-        <script>
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+        <script src="https://code.jquery.com/jquery-3.5.1.min.js"></script>
+        <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
+        <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.min.js" integrity="sha384-B4gt1jrGC7Jh4AgTPSdUtOBvfO8shuf57BaghqFfPlYxofvL8/KUEfYiJOMMV+rV" crossorigin="anonymous"></script>
         <script src="/GRNsight/assets/js/main.js"></script>
         <script src="/GRNsight/assets/js/ga-report.js"></script>
+    
+    
+    
 
 
     </body>

package/_gh_pages/coverage/coverage.json

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