development env path update

Program.cs

@@ -15,7 +15,8 @@ public class Program
         public static void Main(string[] args)
         {
             CreateWebHostBuilder(args)
-                .UseEnvironment("Private")
+                //Change here the environment. Possible values: "Production", "Development", "Private", "Docker"
+                .UseEnvironment("Development")
                 .Build()
                 .Run();
         }

Startup.cs

@@ -51,12 +51,7 @@ public void ConfigureServices(IServiceCollection services)
 
             services.AddMvc().SetCompatibilityVersion(CompatibilityVersion.Version_2_1);
 
-            //if (env.IsDevelopment() || env.IsEnvironment("Private"))
-            //{
-                //Add trailing slash to the end
-                services.Configure<RouteOptions>(options => options.AppendTrailingSlash = true);
-
-            //}
+            //services.Configure<RouteOptions>(options => options.AppendTrailingSlash = true);
 
 
             //services.AddSingleton<IEmailConfiguration>(Configuration.GetSection("EmailConfiguration").Get<EmailConfiguration>());
@@ -79,7 +74,7 @@ public void Configure(IApplicationBuilder app, IHostingEnvironment env)
             } 
             else if (env.IsDevelopment())
             {
-                app.UsePathBase("/coexp_test/");
+                app.UsePathBase("/coexp_test");
                 app.UseHttpsRedirection();
             }
             else if (env.IsEnvironment("Docker"))

Views/Run/Catalogue.cshtml

@@ -26,9 +26,8 @@
             <h5>Please, click the button below to download the gene list of this module:</h5>
             <button id="get_gene_list" type="button" class="btn btn-info">Get Gene List</button>
         </div>
+
         <div id="menu_data">
-            @*<h4>Please, make your selection:</h4>
-            <hr class="menu-hr" />*@
 
             <div id="step1">
                 <span class="fa-li" data-toggle="tooltip"
@@ -39,7 +38,6 @@
                 </span><p class="fa-li-p" for="category_dropdown">Category:</p>
 
                 <select id="category_dropdown" name="category" class="selectpicker" title="Select an option ...">
-                    @*<option></option>*@
                 </select>
             </div><br>
 
@@ -71,16 +69,19 @@
             </div>
 
             <hr class="menu-hr" />
+
             <div id="step4">
                 <button id="send_button" class="btn btn-primary">Accept</button>
             </div>
         </div>
     </div>
 
     <div id="step5" class="col-md-9">
+
         <div id="empty-initial-results">
             <p>Your results will appear here.</p>
         </div>
+
         <!-- Nav tabs -->
         <ul id="tabs" class="nav nav-tabs" style="display:none">
             <li class="active"><a href="#tab1" data-toggle="tab">Ontology view</a></li>
@@ -122,18 +123,15 @@
             <h5>The webmaster has already been informed about this error and it will be sorted shortly. <br />Please, try again later.</h5>
         </div>
 
-        @*<div id="error">
-            <br>
-            <h4>Please, select a module selection type.</h4>
-            <br>
-        </div>*@
     </div>
     <div class="loading_layer"><!-- loading layer --></div>
+
 </div>
 @section HeadStyles{
 
 }
 @section Scripts{
+
     <script type="text/javascript">
         // Turn active current menu's option
         $(".nav-item").find(".active").removeClass("active");
@@ -142,7 +140,11 @@
 
 
     <script type="text/javascript">
+
         $(document).ready(function () {
+
+            // Initiate the tooltips
+
             $('[data-toggle="tooltip"]').tooltip()
 
             $("[data-placement='bottom']").popover();
@@ -161,77 +163,75 @@
                 API.prototype.menuInit(11);
             }
 
-            
-
         });
 
-      function startIntro(){
-        var intro = introJs();
-          intro.setOptions({
-              disableInteraction: true,
-              steps: [
-                  {
-                      element: '#step1',
-                      intro: "<p><b>Category</b></p><p>Please, select here a category of co-expression networks.<br/><br/>It has been pre-selected the <b>'10UKBEC'</b> category. For further information about the networks, please visit the <a href='@Url.Action("Datasets", "Run")' target='_blank'>Datasets</a> section.</p>",
-                      position: 'right',
-                      scrollTo: 'tooltip'
-                  },
-                  {
-                      element: '#step2',
-                      intro: "<b>Network</b><br/><br/>These are all gene co-expression networks that belong to the category selected in the previous step.<br/><br/>It has been pre-selected the <b>'SNIG'</b> network. For further information about the networks, please visit the <a href='@Url.Action("Datasets", "Run")' target='_blank'>Datasets</a> section.</p>",
-                      position: 'right'
-                  },
-                  {
-                      element: '#step3',
-                      intro: "<b>Show results by...</b><br/><br/>These are the different types of results that can be retrieved in this query.<br/><br/>Only the <b>'Gene Ontology'</b> view has been pre-selected by default. You can select only one or both views.",
-                      position: 'right'
-                  },
-                  {
-                      element: '#step4',
-                      intro: "<b>Accept</b><br/><br/>Once you are ready, press this button to submit your query.",
-                      position: 'right'
-                  },
-                  {
-                      element: '#step5',
-                      intro: "<b>Results</b><br/><br/>This is the results area.",
-                      position: 'bottom'
-                  }
-              ]
-          });
-          intro.onbeforechange(function (targetElement) {
+        // Code for the initial tour (i.e. the aid)
+          function startIntro(){
+            var intro = introJs();
+              intro.setOptions({
+                  disableInteraction: true,
+                  steps: [
+                      {
+                          element: '#step1',
+                          intro: "<p><b>Category</b></p><p>Please, select here a category of co-expression networks.<br/><br/>It has been pre-selected the <b>'10UKBEC'</b> category. For further information about the networks, please visit the <a href='@Url.Action("Datasets", "Run")' target='_blank'>Datasets</a> section.</p>",
+                          position: 'right',
+                          scrollTo: 'tooltip'
+                      },
+                      {
+                          element: '#step2',
+                          intro: "<b>Network</b><br/><br/>These are all gene co-expression networks that belong to the category selected in the previous step.<br/><br/>It has been pre-selected the <b>'SNIG'</b> network. For further information about the networks, please visit the <a href='@Url.Action("Datasets", "Run")' target='_blank'>Datasets</a> section.</p>",
+                          position: 'right'
+                      },
+                      {
+                          element: '#step3',
+                          intro: "<b>Show results by...</b><br/><br/>These are the different types of results that can be retrieved in this query.<br/><br/>Only the <b>'Gene Ontology'</b> view has been pre-selected by default. You can select only one or both views.",
+                          position: 'right'
+                      },
+                      {
+                          element: '#step4',
+                          intro: "<b>Accept</b><br/><br/>Once you are ready, press this button to submit your query.",
+                          position: 'right'
+                      },
+                      {
+                          element: '#step5',
+                          intro: "<b>Results</b><br/><br/>This is the results area.",
+                          position: 'bottom'
+                      }
+                  ]
+              });
+              intro.onbeforechange(function (targetElement) {
               
-              if (targetElement.id == "step2" && $("#category_dropdown").val() == "10UKBEC") {
-                  $('#network_dropdown').val('SNIG').change();
-                  $('#network_dropdown')
-                      .prop("disabled", false)
-                      .selectpicker('refresh');
-              }
-              if (targetElement.id == "step3") {
-                  $('#view_selection').val('1').change();
-                  $('#view_selection')
-                      .selectpicker('refresh');
-              }
-          });
-
+                  if (targetElement.id == "step2" && $("#category_dropdown").val() == "10UKBEC") {
+                      $('#network_dropdown').val('SNIG').change();
+                      $('#network_dropdown')
+                          .prop("disabled", false)
+                          .selectpicker('refresh');
+                  }
+                  if (targetElement.id == "step3") {
+                      $('#view_selection').val('1').change();
+                      $('#view_selection')
+                          .selectpicker('refresh');
+                  }
+              });
 
-        var doneTourCatalogue = sessionStorage.getItem('EventTourCatalogue') === 'Completed';
-          if (doneTourCatalogue) {
-            return;
-            }
-          else {
-              if (environment != "ATN_5843218Gt") {
-                  intro.start();
+              var doneTourCatalogue = sessionStorage.getItem('EventTourCatalogue') === 'Completed';
+              if (doneTourCatalogue) {
+                  return;
+              }
+              else {
+                  if (environment != "ATN_5843218Gt") {
+                      intro.start();
 
-                  intro.oncomplete(function () {
-                      sessionStorage.setItem('EventTourCatalogue', 'Completed');
-                  });
+                      intro.oncomplete(function () {
+                          sessionStorage.setItem('EventTourCatalogue', 'Completed');
+                      });
 
-                  intro.onexit(function () {
-                      sessionStorage.setItem('EventTourCatalogue', 'Completed');
-                  });
+                      intro.onexit(function () {
+                          sessionStorage.setItem('EventTourCatalogue', 'Completed');
+                      });
+                  }
               }
-        }
-      }
+          }
 
     </script>
 }

obj/CoExp_Web.csproj.nuget.dgspec.json

@@ -70,7 +70,7 @@
           ],
           "assetTargetFallback": true,
           "warn": true,
-          "runtimeIdentifierGraphPath": "C:\\Program Files\\dotnet\\sdk\\5.0.101\\RuntimeIdentifierGraph.json"
+          "runtimeIdentifierGraphPath": "C:\\Program Files\\dotnet\\sdk\\5.0.102\\RuntimeIdentifierGraph.json"
         }
       }
     }

obj/CoExp_Web.csproj.nuget.g.props

@@ -7,7 +7,7 @@
     <NuGetPackageRoot Condition=" '$(NuGetPackageRoot)' == '' ">$(UserProfile)\.nuget\packages\</NuGetPackageRoot>
     <NuGetPackageFolders Condition=" '$(NuGetPackageFolders)' == '' ">C:\Users\skgtsg0\.nuget\packages\;C:\Program Files\dotnet\sdk\NuGetFallbackFolder</NuGetPackageFolders>
     <NuGetProjectStyle Condition=" '$(NuGetProjectStyle)' == '' ">PackageReference</NuGetProjectStyle>
-    <NuGetToolVersion Condition=" '$(NuGetToolVersion)' == '' ">5.8.0</NuGetToolVersion>
+    <NuGetToolVersion Condition=" '$(NuGetToolVersion)' == '' ">5.8.1</NuGetToolVersion>
   </PropertyGroup>
   <ItemGroup Condition=" '$(ExcludeRestorePackageImports)' != 'true' ">
     <SourceRoot Include="$([MSBuild]::EnsureTrailingSlash($(NuGetPackageFolders)))" />

obj/project.assets.json

@@ -12603,7 +12603,7 @@
         ],
         "assetTargetFallback": true,
         "warn": true,
-        "runtimeIdentifierGraphPath": "C:\\Program Files\\dotnet\\sdk\\5.0.101\\RuntimeIdentifierGraph.json"
+        "runtimeIdentifierGraphPath": "C:\\Program Files\\dotnet\\sdk\\5.0.102\\RuntimeIdentifierGraph.json"
       }
     }
   }

wwwroot/js/api.js

@@ -253,23 +253,7 @@ API.prototype.menuInit = function (view) {
     $('#send_button').on('click', function () {
         API.prototype.sendButtonFunction(view);
     });
-    //When the user press the 'Save Plot' button (in 'Plot' view):
-    //$('#save_plot').on('click', function () {
-
-    //    var blob = new Blob(["Hello, world!"], { type: "text/plain;charset=utf-8" });
-    //    saveAs(blob, "hello world.txt");
-    //    //var b64key = 'base64,';
-    //    //var b64 = cy.png().substring( cy.png().indexOf(b64key) + b64key.length );
-    //    //var imgBlob = base64ToBlob(b64, 'image/png');
-
-    //    //saveAs(imgBlob, 'graph.png');
-    //});
-    ////When the user press the 'Save Data' button (in 'Plot' view):
-    //$('#save_data').on('click', function () {
-    //    var jsonBlob = new Blob([JSON.stringify(cy.json())], { type: 'application/javascript;charset=utf-8' });
 
-    //    saveAs(jsonBlob, 'graph.json');
-    //});
 
     // Add event listener for opening and closing table details
     $('#goFromTissue_table').on('click', 'td.details-control', function () {
@@ -535,6 +519,7 @@ API.prototype.getModuleTOMGenes = function (category, network, module) {
         });
     }
 }
+
 /**
  * This function requests all data in a tree-menu format and fills it.
  */
@@ -1766,8 +1751,7 @@ API.prototype.hideRowsReportOnGenes = function (d, tr, row, id) {/* Formatting f
  * @param {string} term Gene name.
  */
 API.prototype.getCardData = function (term) {
-
-
+
     let url = '/' + environment + '/API/GetInfoFromQuickGO';
 
     $.ajax({
@@ -1875,29 +1859,6 @@ API.prototype.generateGraph = function () {
     }
 }
 
-///**
-// * Function to download the plot's raw data. The data is downloaded using a xlsx file. 
-// */
-//API.prototype.downloadSVGData = function () {
-
-//    /* make the worksheet */
-//    const ws = XLSX.utils.json_to_sheet(SVGData.nodes, { header: Object.keys(SVGData.nodes[1]) })
-
-//    /* add to workbook */
-//    const wb = XLSX.utils.book_new();
-//    XLSX.utils.book_append_sheet(wb, ws, "CoExpData");
-
-//    const category = $('#category_dropdown').find(":selected").val();
-//    const network = $('#network_dropdown').find(":selected").val();
-//    const moduleColor = $('#module_dropdown').find(":selected").val();
-//    const top = $('#text-box_genes-range').val();
-//    var dt = new Date();
-//    var time = dt.getDay() + "-" + dt.getMonth() + "-" + dt.getFullYear()
-//    const fileName = category + '_' + network + '_' + moduleColor + '_' + top + 'genes_' + time + '.xlsx';
-
-//    /* generate an XLSX file */
-//    XLSX.writeFile(wb, fileName); 
-//}
 
 API.prototype.getMM = function (network, category, module) {
 
@@ -1965,42 +1926,6 @@ API.prototype.getMM = function (network, category, module) {
         });
 }
 
-//API.prototype.sendFeedback = function() {
-
-//    let comments = $("#feedback_comments").val();
-//    let grade_experience = $('input[name=feedback_radio]:checked').val()
-//    let name_feedback = $('#feedback_name').val()
-//    let email_feedback = $('#feedback_email').val()
-//    var email_regex = /^([a-zA-Z0-9_\.\-\+])+\@(([a-zA-Z0-9\-])+\.)+([a-zA-Z0-9]{2,4})+$/;
-
-//    if (name_feedback == "") {
-//        alert("Please, introduce your name.")
-//    } else if (email_feedback == "") {
-//        alert("Please, introduce your email.")
-//    } else if (comments == "") {
-//        alert("Please, introduce your comments.")
-//    } else if (!email_regex.test(email_feedback)) {
-//        alert("You have entered an invalid e-mail address. Please, try it again.")
-//    } else {
-
-//        //Make a request to CoExp-R-software's API
-//        $.ajax({
-//            url: '/' + environment + '/API/SendFeedback?Name=' + name_feedback + '&Address=' + email_feedback
-//                +'&Subject=CoExp_Feedback&Content=' + comments + '&LevelSatisfaction=' + grade_experience,
-//            type: 'GET',
-//            success: function (data) {
-//                alert("Your feedback has been successfully sent! Thanks for taking the time to provide it!\n")
-//                $("#close_feedback").trigger("click")
-//            },
-//            error: function (data) {
-//                //If an error occurs:
-//                alert("Sorry, an error has occurred. You may have entered an invalid e-mail address. Please, try it again.")
-//                console.log(data);
-//            }
-//        });
-//    }
-//};
-
 API.prototype.arrayDiff = function (array1, array2) {
     var ret = [];
     for (var i in array1) {