Merge branch 'master' into unstable

iVis-at-Bilkent · Sep 3, 2024 · d5876a1 · d5876a1
2 parents e568157 + 98af7d0
commit d5876a1
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Showing 5 changed files with 69 additions and 14 deletions.
diff --git a/app/js/ajax-utilities.js b/app/js/ajax-utilities.js
@@ -128,8 +128,8 @@ exports.sendEmail = function(req, res){
 	var attachment = fileContent == "no-data" ? false : true;
 	let mailOptions = {
 		// should be replaced with real recipient's account
-		//to: 'replyto.lcsb.gitlab+minerva-core-499-3hxqgkf3oh3yq2zb9veolqjo6-issue@gmail.com',
-		to: "newteditor@gmail.com",
+		to: 'replyto.lcsb.gitlab+minerva-core-499-3hxqgkf3oh3yq2zb9veolqjo6-issue@gmail.com',
+		//to: "newteditor@gmail.com",
 		cc: 'newteditor@gmail.com',	
 		subject: "Error Report From Newt",		
 		text: req.body.message,

diff --git a/app/js/app-menu.js b/app/js/app-menu.js
@@ -648,6 +648,33 @@ module.exports = function() {
       }
     });
 
+    $("#gpml-file-input").change(function () {
+
+      var chiseInstance = appUtilities.getActiveChiseInstance();
+      var cy = appUtilities.getActiveCy();
+      if ($(this).val() != "") {
+        var file = this.files[0];
+        appUtilities.setFileContent(file.name);
+        chiseInstance.loadGpml(file,  success = function(data){
+          if (cy.elements().length !== 0) {
+            promptConfirmationView.render(function () {
+              chiseInstance.loadSBGNMLText(data.message, false, file.name, cy);
+            });
+          }
+          else {
+            chiseInstance.loadSBGNMLText(data.message, false, file.name, cy);
+          }
+        },
+        error = function(data){
+          promptFileConversionErrorView.render();          
+          document.getElementById("file-conversion-error-message").innerText = "Conversion service is not available!";
+
+        });
+
+        $(this).val("");
+      }
+    });
+
     $("#simple-af-file-input").change(function () {
       var chiseInstance = appUtilities.getActiveChiseInstance();
 
@@ -791,6 +818,18 @@ module.exports = function() {
         // clear urlParams from scratch
         appUtilities.setScratch(cy, 'urlParams', undefined);
 
+
+        // get applyLayout value before map properties are filtered, apply layout
+        // isn't really a map property so its not added to sbgnviz 
+        // validMapProperties
+        const applyLayout = urlParams.applyLayoutOnURL === "true";
+        const fromURL = urlParams.url !== undefined;
+
+        if (urlParams.compoundPadding) {
+          const compoundPadding = urlParams.compoundPadding;
+          chiseInstance.setCompoundPadding(Number(compoundPadding));
+        }
+
         // filter map properties from the url parameters
 
         // get applyLayout value before map properties are filtered, apply layout
@@ -829,6 +868,24 @@ module.exports = function() {
           appUtilities.applyMapColorScheme(urlParams.mapColorScheme, currentGeneralProperties.mapColorSchemeStyle, appUtilities.colorSchemeInspectorView);
         }
 
+        if (fromURL && applyLayout) {
+          let currentLayoutProperties = appUtilities.getScratch(cy, 'currentLayoutProperties');
+
+          // Below is copied from sbgnviz.graphUtilities.updateGraph
+          let preferences = {};
+          if(cy.nodes().length > 3000 || cy.edges().length > 3000) {
+            preferences.quality = "draft";
+          }
+          preferences.animate = false;
+          preferences.randomize = true;
+          preferences = $.extend({}, currentLayoutProperties, preferences);
+          layoutPropertiesView.applyLayout(preferences);
+        }
+
+        if (urlParams.mapColorScheme) {
+          appUtilities.applyMapColorScheme(urlParams.mapColorScheme, currentGeneralProperties.mapColorSchemeStyle, appUtilities.colorSchemeInspectorView);
+        }
+
         // merge the map properties coming from url into
         // the map properties read from file
         for ( var prop in mapPropsFromUrl ) {

diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js
@@ -3067,7 +3067,7 @@ appUtilities.launchWithModelFile = function() {
    function loadFromURL(filepath, chiseInstance, promptInvalidURLWarning){
 
    chiseInstance.startSpinner('paths-byURL-spinner');
-  
+
     var loadCallbackSBGNMLValidity = function (text) {
       $.ajax({
         type: 'post',
@@ -3121,7 +3121,6 @@ appUtilities.launchWithModelFile = function() {
           chiseInstance.showSpinnerText('paths-byURL-spinner')
         }
 
-
         if (!data.error && data.response.statusCode == 200 && data.response.body) {
           $(document).trigger('sbgnvizLoadFromURL', [filename, cyInstance]);
           const fileContents = data.response.body;
@@ -3244,7 +3243,6 @@ appUtilities.launchWithModelFile = function() {
       error: function(xhr, options, err){
         loadCallbackInvalidityWarning();
         chiseInstance.endSpinner("paths-byURL-spinner");
-
       }
     });
   }

diff --git a/index.html b/index.html
@@ -521,7 +521,7 @@
           </div>
         </nav>
       </div>
-
+      
       <div id="sbgn-toolbar" class="read-mode-off">
         <div class="inside-menu">
           <div style="padding: 1px" class="sbgn-toolbar-element">

diff --git a/package.json b/package.json
@@ -22,13 +22,13 @@
     "backbone": "1.3.3",
     "body-parser": "^1.19.0",
     "bootstrap": "3.3.7",
-    "chise": "github:iVis-at-Bilkent/chise.js#unstable",
+    "chise": "^3.0.0",
     "chroma-js": "^1.3.4",
-    "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#unstable",
-    "cytoscape-autopan-on-drag": "github:iVis-at-Bilkent/cytoscape.js-autopan-on-drag#unstable",
-    "cytoscape-clipboard": "github:iVis-at-Bilkent/cytoscape.js-clipboard#unstable",
-    "cytoscape-context-menus": "github:iVis-at-Bilkent/cytoscape.js-context-menus#unstable",
-    "cytoscape-edge-editing": "github:iVis-at-Bilkent/cytoscape.js-edge-editing#unstable",
+    "cytoscape": "github:iVis-at-Bilkent/cytoscape.js#master",
+    "cytoscape-autopan-on-drag": "2.2.1",
+    "cytoscape-clipboard": "2.2.1",
+    "cytoscape-context-menus": "3.1.0",
+    "cytoscape-edge-editing": "2.0.1",
     "cytoscape-edgehandles": "~2.13.1",
     "cytoscape-expand-collapse": "github:iVis-at-Bilkent/cytoscape.js-expand-collapse#unstable",
     "cytoscape-fcose": "github:iVis-at-Bilkent/cytoscape.js-fcose#unstable",
@@ -38,8 +38,8 @@
     "cytoscape-node-editing": "github:iVis-at-Bilkent/cytoscape.js-node-editing#unstable",
     "cytoscape-panzoom": "~2.5.2",
     "cytoscape-popper": "^1.0.2",
-    "cytoscape-undo-redo": "github:iVis-at-Bilkent/cytoscape.js-undo-redo#unstable",
-    "cytoscape-view-utilities": "github:iVis-at-Bilkent/cytoscape.js-view-utilities#unstable",
+    "cytoscape-undo-redo": "1.3.3",
+    "cytoscape-view-utilities": "4.1.0",
     "file-saver": "^2.0.2",
     "intro.js": "2.9.3",
     "jquery": "~3.3.1",