Changes for #712 Item 6: Added pop-up error for wrong SIF style,layou…

…t imports. Item 2: Using Minerva when converting SBML to .sbgnml
iVis-at-Bilkent · Jul 4, 2024 · 9ec0cb4 · 9ec0cb4
1 parent 5fe2cd0
commit 9ec0cb4
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Showing 3 changed files with 112 additions and 11 deletions.
diff --git a/app/js/app-menu.js b/app/js/app-menu.js
@@ -13,7 +13,7 @@ module.exports = function() {
   var dynamicResize = appUtilities.dynamicResize.bind(appUtilities);
 
   var layoutPropertiesView, generalPropertiesView,neighborhoodQueryView, pathsBetweenQueryView, pathsFromToQueryView, commonStreamQueryView, pathsByURIQueryView,  promptSaveView, promptConfirmationView,
-        promptMapTypeView, promptInvalidTypeWarning, promtErrorPD2AF, promptInvalidFileView, promptFileConversionErrorView, promptInvalidURIWarning, reactionTemplateView, gridPropertiesView, fontPropertiesView, fileSaveView,saveUserPreferencesView, loadUserPreferencesView;
+        promptMapTypeView, promptInvalidTypeWarning, promtErrorPD2AF, promptInvalidFileView, promptFileConversionErrorView, promptInvalidURIWarning, reactionTemplateView, gridPropertiesView, fontPropertiesView, fileSaveView,saveUserPreferencesView, loadUserPreferencesView, sifMapWarning;
 
   function validateSBGNML(xml) {
     $.ajax({
@@ -158,6 +158,7 @@ module.exports = function() {
   promptMapTypeView = appUtilities.promptMapTypeView = new BackboneViews.PromptMapTypeView({el: '#prompt-mapType-table'});
   promptInvalidFileView = appUtilities.promptInvalidFileView = new BackboneViews.PromptInvalidFileView({el: '#prompt-invalidFile-table'});
   promptInvalidTypeWarning = appUtilities.promptInvalidTypeWarning = new BackboneViews.PromptInvalidTypeWarning({el: '#prompt-errorInvalidType-table'});
+  sifMapWarning = appUtilities.sifMapWarning = new BackboneViews.SifMapWarning({el: '#errorSifMap-table'});
   promtErrorPD2AF = appUtilities.promtErrorPD2AF = new BackboneViews.PromtErrorPD2AF({el: '#prompt-errorPD2AF-table'});
   promptFileConversionErrorView = appUtilities.promptFileConversionErrorView = new BackboneViews.PromptFileConversionErrorView({el: '#prompt-fileConversionError-table'});
   reactionTemplateView = appUtilities.reactionTemplateView = new BackboneViews.ReactionTemplateView({el: '#sbgn-bricks-table'});
@@ -450,10 +451,22 @@ module.exports = function() {
     });
 
     $("#import-sif-style").click(function () {
+      //Check if current map type is SIF
+      var mapType = appUtilities.getActiveChiseInstance().elementUtilities.mapType;
+      if (mapType != "SIF") {
+        sifMapWarning.render();
+        return;
+      }
       $("#sif-style-input").trigger('click');
     });
 
     $("#import-sif-layout").click(function () {
+      //Check if current map type is SIF
+      var mapType = appUtilities.getActiveChiseInstance().elementUtilities.mapType;
+      if (mapType != "SIF") {
+        sifMapWarning.render();
+        return;
+      }
       $("#sif-layout-input").trigger('click');
     });
 

diff --git a/app/js/backbone-views.js b/app/js/backbone-views.js
@@ -3225,7 +3225,7 @@ var FileSaveView = Backbone.View.extend({
     self.template = _.template($("#file-save-template").html());
 
     // Check for unsupported conversions
-    map_type = appUtilities.getActiveChiseInstance().elementUtilities.mapType;
+    mapType = appUtilities.getActiveChiseInstance().elementUtilities.mapType;
     var unsupportedConversions = {
       "PD": ["sif", "sifLayout"],
       "AF": ["sif", "sifLayout", "sbml", "celldesigner", "gpml"],
@@ -3235,7 +3235,7 @@ var FileSaveView = Backbone.View.extend({
       "HybridAny": ["sbgn", "sif", "sifLayout", "sbml", "celldesigner", "gpml"]
     };
 
-    if (unsupportedConversions[map_type] && unsupportedConversions[map_type].includes(fileformat)) {
+    if (unsupportedConversions[mapType] && unsupportedConversions[mapType].includes(fileformat)) {
         var exportErrorView = new ExportErrorView({el: "#exportError-table",});
         exportErrorView.render();          
         document.getElementById("export-error-message").innerText = "Not applicable for the current map type!";
@@ -3331,6 +3331,20 @@ var FileSaveView = Backbone.View.extend({
 
           var saveAsFcn = chiseInstance.saveAsNwt;
           if (fileformat === "sbgn") {
+            if (chiseInstance.elementUtilities.mapType === "SBML") {
+            console.log("fileformat is sbgn and maptype is SBML");
+              chiseInstance.saveAsSbgnmlForSBML(filename, function () {
+                var promptSbmlConversionErrorView =
+                  new PromptSbmlConversionErrorView({
+                    el: "#prompt-sbmlConversionError-table",
+                  });
+                promptSbmlConversionErrorView.render();
+                document.getElementById("file-conversion-error-message").innerText =
+                  "Conversion service is not available!";
+              }
+              );
+              return;
+            }
             saveAsFcn = chiseInstance.saveAsSbgnml;
           }
 
@@ -3394,14 +3408,27 @@ var FileSaveView = Backbone.View.extend({
               "Conversion service is not available!";
           });
         } else if (fileformat === "sbml") {
-          chiseInstance.saveAsSbml(filename, function (data, errorMessage) {
-            var promptSbmlConversionErrorView =
-              new PromptSbmlConversionErrorView({
-                el: "#prompt-sbmlConversionError-table",
-              });
-            promptSbmlConversionErrorView.render(data, errorMessage);
-            //document.getElementById("file-conversion-error-message").innerText = "Conversion service is not available!";
-          });
+
+          if (mapType === "PD") {
+            chiseInstance.saveAsSbml(filename, function (data, errorMessage) {
+              var promptSbmlConversionErrorView =
+                new PromptSbmlConversionErrorView({
+                  el: "#prompt-sbmlConversionError-table",
+                });
+              promptSbmlConversionErrorView.render(data, errorMessage);
+              //document.getElementById("file-conversion-error-message").innerText = "Conversion service is not available!";
+            });
+          } else if (mapType === "SBML") {
+            chiseInstance.saveSbmlForSBML(filename, function (data, errorMessage) {
+              var promptSbmlConversionErrorView =
+                new PromptSbmlConversionErrorView({
+                  el: "#prompt-sbmlConversionError-table",
+                });
+              promptSbmlConversionErrorView.render(data, errorMessage);
+              //document.getElementById("file-conversion-error-message").innerText = "Conversion service is not available!";
+            });
+          }
+
         } else if (fileformat === "gpml") {
           chiseInstance.saveAsGpml(filename, function (data, errorMessage) {
             var promptSbmlConversionErrorView =
@@ -4335,6 +4362,30 @@ var PromptInvalidTypeWarning = Backbone.View.extend({
     return this;
   },
 });
+
+var SifMapWarning = Backbone.View.extend({
+  initialize: function () {
+    var self = this;
+    self.template = _.template($("#sifMapWarning-template").html());
+  },
+  render: function () {
+    var self = this;
+    self.template = _.template($("#sifMapWarning-template").html());
+
+    $(self.el).html(self.template);
+    $(self.el).modal("show");
+
+    $(document)
+      .off("click", "#sifMapWarning-confirm")
+      .on("click", "#sifMapWarning-confirm", function (evt) {
+        $(self.el).modal("toggle");
+      });
+
+    return this;
+  },
+});
+
+
 var PromtErrorPD2AF = Backbone.View.extend({
   initialize: function () {
     var self = this;
@@ -6940,6 +6991,7 @@ module.exports = {
   PromptMapTypeView: PromptMapTypeView,
   PromptInvalidFileView: PromptInvalidFileView,
   PromptInvalidTypeWarning: PromptInvalidTypeWarning,
+  SifMapWarning: SifMapWarning,
   PromtErrorPD2AF: PromtErrorPD2AF,
   PromptFileConversionErrorView: PromptFileConversionErrorView,
   ExportErrorView: ExportErrorView,

diff --git a/index.html b/index.html
@@ -2588,6 +2588,13 @@
     >
       <!-- map type change confirmation dialog will be shown here-->
     </div>
+    <div
+    id="errorSifMap-table"
+    tabindex="-1"
+    class="modal fade"
+    role="dialog"
+  >
+  </div>
     <div
       id="prompt-errorPD2AF-table"
       tabindex="-1"
@@ -4470,7 +4477,36 @@ <h4 class="modal-title">Error</h4>
           </div>
       </div>
     </script>
+    <!-- SIF Map Warning-->
+    <script type="text/template" id="sifMapWarning-template">
+      <div class="modal-dialog sbgn-modal-dialog" style="width: 335px;">
+      <div class="modal-content">
+      <div class="modal-header">
+      <button type="button" class="close" data-dismiss="modal">&times;</button>
+      <h4 class="modal-title">Error</h4>
+      </div>
+      <div class="modal-body">
+      <table class="table-condensed layout-table dialog-table" style="margin: auto;">
+      <tbody>
+      <tr>
+      <th style="padding-left: 0px;" align="left">
+      <span class="add-on layout-text centered">Can only be used on SIF maps!</span>
+      </th>
+      </tr>
 
+      <tr id="sifMapWarning-buttons" style="padding-bottom: 0px; margin-bottom: 0px;">
+      <td>
+      </td>
+      </tr>
+      </tbody>
+      </table>
+      </div>
+      <div class="modal-footer" style="text-align: center">
+      <button id="sifMapWarning-confirm" class="btn btn-default">OK</button>
+      </div>
+      </div>
+      </div>
+    </script>
     <!-- Invalid Map Type Warning-->
     <script type="text/template" id="prompt-errorInvalidType-template">
       <div class="modal-dialog sbgn-modal-dialog" style="width: 335px;">