clean scripts for fewer js errors

src/main/resources/projects/CA1/3.json

@@ -1,16 +1,41 @@
-{ "activeExperimentId" : 1,
-  "experiments" : [ { "aspectConfigurations" : [  ],
-        "description" : "Hippocampus CA1 pyramidal cell from M. Migliore, M. Ferrante, GA Ascoli (2005). The model shows how the back- and forward propagation of action potentials in the oblique dendrites of CA1 neurons could be modulated by local properties such as morphology or active conductances. The model was converted to NeuroML (Source: <a target='_blank' href='http://opensourcebrain.org/projects/ca1pyramidalcell'>Open Source Brain</a>)",
-        "id" : 1,
-        "lastModified" : "1436102517799",
-        "name" : "CA1 Experiment",
-        "script" : "/projects/CA1/script.js",
-        "status" : "COMPLETED"
-      } ],
-  "geppettoModel" : { "id" : 9,
-      "type" : "GEPPETTO_PROJECT",
-      "url" : "/projects/CA1/GeppettoModel.xmi"
-    },
-  "id" : 3,
-  "name" : "CA1 Pyramidal Cell"
+{ "activeExperimentId" : 1,
+  "experiments" : [ { "aspectConfigurations" : [  ],
+	  "view": {
+	        "id": 1,
+	        "viewStates": {
+	          "views": {
+	            "TreeVisualiserDAT1": {
+	              "widgetType": 3,
+	              "isWidget": true,
+	              "transparentBackground": false,
+	              "name": "Hippocampus CA1 pyramidal cell model",
+	              "size": {
+	                "height": 448,
+	                "width": 452
+	              },
+	              "position": {
+	                "left": 147,
+	                "top": 90
+	              },
+	              "dataType": "object",
+	              "data": [
+	                "ca1.getType()"
+	              ]
+	            }
+	          }
+	        }
+	      },
+        "description" : "Hippocampus CA1 pyramidal cell from M. Migliore, M. Ferrante, GA Ascoli (2005). The model shows how the back- and forward propagation of action potentials in the oblique dendrites of CA1 neurons could be modulated by local properties such as morphology or active conductances. The model was converted to NeuroML (Source: <a target='_blank' href='http://opensourcebrain.org/projects/ca1pyramidalcell'>Open Source Brain</a>)",
+        "id" : 1,
+        "lastModified" : "1436102517799",
+        "name" : "CA1 Experiment",
+        "script" : "/projects/CA1/script.js",
+        "status" : "COMPLETED"
+      } ],
+  "geppettoModel" : { "id" : 9,
+      "type" : "GEPPETTO_PROJECT",
+      "url" : "/projects/CA1/GeppettoModel.xmi"
+    },
+  "id" : 3,
+  "name" : "CA1 Pyramidal Cell"
 }

src/main/resources/projects/CA1/script.js

@@ -1,11 +0,0 @@
-G.addWidget(3,{isStateless:true}).setData(ca1.getType(),{expandNodes:true});
-TreeVisualiserDAT1.setPosition(147,90);
-TreeVisualiserDAT1.setSize(448,452);
-TreeVisualiserDAT1.setName("Hippocampus CA1 pyramidal cell model");
-
-Model.neuroml.morphology_CA1.kad_dendrite_group.show(true)
-var newPopup = G.addWidget(1,{isStateless:true});
-newPopup.setMessage(Project.getActiveExperiment().getDescription());
-newPopup.setPosition(950,98);
-newPopup.setSize(138,500);
-newPopup.setName("Description");

src/main/resources/projects/CElegansMuscleModel/4.json

@@ -15,11 +15,33 @@
                   "net1.muscle[0].biophys.membraneProperties.ca_boyle_all.iDensity"
                 ]
             } ],
+            "view": {
+	        "id": 1,
+	        "viewStates": {
+	          "views": {
+	            "Popup1": {
+	              "widgetType": 1,
+	              "isWidget": true,
+	              "transparentBackground": false,
+	              "name": "Description",
+	              "size": {
+	                "height": 160,
+	                "width": 446
+	              },
+	              "position": {
+	                "left": 147,
+	                "top": 90
+	              },
+	              "dataType": "stringCommand",
+	              "data": "Project.getActiveExperiment().getDescription()"
+	            }
+	          }
+	        }
+	      },
         "description" : "This project is based on the <a href=\"http://github.com/openworm/muscle_model\">OpenWorm muscle model</a>.  This simulates the electrical properties of a single C. elegans body wall muscle cell.  The simulation was executed using NEURON. The original version is based on a paper by Boyle & Cohen in 2008.",
         "id" : 1,
         "lastModified" : "1436102517799",
         "name" : "Muscle cell NEURON simulation",
-        "script" : "/projects/CElegansMuscleModel/script.js",
         "simulationResults" : [ { "format" : "GEPPETTO_RECORDING",
               "id" : 1,
               "result" : { "id" : 1,

src/main/resources/projects/EyeWireGanglionCell/9.json

@@ -1,16 +1,38 @@
-{ "activeExperimentId" : 1,
-  "experiments" : [ { "aspectConfigurations" : [  ],
-        "description" : "<a href=\"https://eyewire.org\">EyeWire</a> is a game to map the brain from Sebastian Seung's Lab at MIT. This citizen science human-based computation game challenges players to map 3D neurons in a retina. Geppetto is visualizing in 3D a morphology of a Ganglion cell that was reconstructed using the game.",
-        "id" : 1,
-        "lastModified" : "1436102517799",
-        "name" : "Only morphology, no simulation",
-        "script" : "/projects/EyeWireGanglionCell/script.js",
-        "status" : "COMPLETED"
-      } ],
-  "geppettoModel" : { "id" : 9,
-      "type" : "GEPPETTO_PROJECT",
-      "url" : "/projects/EyeWireGanglionCell/GeppettoModel.xmi"
-    },
-  "id" : 9,
-  "name" : "Ganglion Cell from EyeWire"
+{ "activeExperimentId" : 1,
+  "experiments" : [ { "aspectConfigurations" : [  ],
+	  "view": {
+	        "id": 1,
+	        "viewStates": {
+	          "views": {
+	            "Popup1": {
+	              "widgetType": 1,
+	              "isWidget": true,
+	              "transparentBackground": false,
+	              "name": "EyeWire Sample",
+	              "size": {
+	                "height": 172,
+	                "width": 394
+	              },
+	              "position": {
+	                "left": 147,
+	                "top": 90
+	              },
+	              "dataType": "stringCommand",
+	              "data":"Project.getActiveExperiment().getDescription()"
+	            }
+	          }
+	        }
+	      },
+        "description" : "<a href=\"https://eyewire.org\">EyeWire</a> is a game to map the brain from Sebastian Seung's Lab at MIT. This citizen science human-based computation game challenges players to map 3D neurons in a retina. Geppetto is visualizing in 3D a morphology of a Ganglion cell that was reconstructed using the game.",
+        "id" : 1,
+        "lastModified" : "1436102517799",
+        "name" : "Only morphology, no simulation",
+        "status" : "COMPLETED"
+      } ],
+  "geppettoModel" : { "id" : 9,
+      "type" : "GEPPETTO_PROJECT",
+      "url" : "/projects/EyeWireGanglionCell/GeppettoModel.xmi"
+    },
+  "id" : 9,
+  "name" : "Ganglion Cell from EyeWire"
 }

src/main/resources/projects/EyeWireGanglionCell/script.js

@@ -1,13 +1,8 @@
-G.addWidget(Widgets.POPUP);
-Popup1.setName("EyeWire Sample");
-Popup1.setMessage(Project.getActiveExperiment().getDescription());
-Popup1.setSize(172.80000019073486,394.80000019073486)
-Popup1.setPosition(129,77)
-G.incrementCameraZoom(-0.16)
-G.incrementCameraRotate(0, 0, 0.07)
-$(".simulation-controls").children().attr('disabled', 'disabled')
-$("#genericHelpBtn").removeAttr('disabled')
-G.setCameraPosition(-7197.325,144949.009,101269.908)
-G.setCameraRotation(2.961,-1.114,1.791,75645.966)
-GEPPETTO.SceneController.setWireframe(true);
-G.autoRotate();
+Canvas1.incrementCameraZoom(-0.16)
+Canvas1.incrementCameraRotate(0, 0, 0.07)
+$(".simulation-controls").children().attr('disabled', 'disabled')
+$("#genericHelpBtn").removeAttr('disabled')
+Canvas1.setCameraPosition(-7197.325,144949.009,101269.908)
+Canvas1.setCameraRotation(2.961,-1.114,1.791,75645.966)
+GEPPETTO.SceneController.setWireframe(true);
+Canvas1.autoRotate();

src/main/resources/projects/Pharyngeal/PharyngealNetworkcadb5b76a8857af6815e279d2f2ea674.js

@@ -1 +0,0 @@
-initOSBGeppetto("network", PharyngealNetwork);

src/main/resources/projects/cElegansConnectome/16.json

@@ -1,26 +1,48 @@
-{ "activeExperimentId" : 1,
-  "experiments" : [ { "aspectConfigurations" : [ { "id" : 1,
-              "instance" : "c302",
-              "simulatorConfiguration" : { "conversionServiceId" : "lemsConversion",
-                  "id" : 1,
-                  "length" : 0,
-                  "parameters" : { "target" : "network_CElegans" },
-                  "simulatorId" : "neuronSimulator",
-                  "timestep" : 0.0001
-                },
-              "watchedVariables" : [  ]
-            } ],
-        "description" : "Caenorhabditis elegans is a free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments. This network model of its nervous system was generated using <a target='_blank' href='https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302'>c302</a>, an experimental framework from the <a target='_blank' href='http://openworm.org'>OpenWorm</a> project for generating network models in NeuroML 2 based on C. elegans connectivity data.",
-        "id" : 1,
-        "lastModified" : "1436102517799",
-        "name" : "C. elegans connectome",
-        "script" : "/projects/cElegansConnectome/script.js",
-        "status" : "COMPLETED"
-      } ],
-  "geppettoModel" : { "id" : 6,
-      "type" : "GEPPETTO_PROJECT",
-      "url" : "/projects/cElegansConnectome/GeppettoModel.xmi"
-    },
-  "id" : 16,
-  "name" : "C. elegans multi-compartment connectome"
+{ "activeExperimentId" : 1,
+  "experiments" : [ { "aspectConfigurations" : [ { "id" : 1,
+              "instance" : "c302",
+              "simulatorConfiguration" : { "conversionServiceId" : "lemsConversion",
+                  "id" : 1,
+                  "length" : 0,
+                  "parameters" : { "target" : "network_CElegans" },
+                  "simulatorId" : "neuronSimulator",
+                  "timestep" : 0.0001
+                },
+              "watchedVariables" : [  ]
+            } ],
+            "view": {
+	        "id": 1,
+	        "viewStates": {
+	          "views": {
+	            "Popup1": {
+	              "widgetType": 1,
+	              "isWidget": true,
+	              "transparentBackground": false,
+	              "name": "Description",
+	              "size": {
+	                "height": 172,
+	                "width": 394
+	              },
+	              "position": {
+	                "left": 147,
+	                "top": 90
+	              },
+	              "dataType": "stringCommand",
+	              "data": "Project.getActiveExperiment().getDescription()"
+	            }
+	          }
+	        }
+	      },
+        "description" : "Caenorhabditis elegans is a free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments. This network model of its nervous system was generated using <a target='_blank' href='https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302'>c302</a>, an experimental framework from the <a target='_blank' href='http://openworm.org'>OpenWorm</a> project for generating network models in NeuroML 2 based on C. elegans connectivity data.",
+        "id" : 1,
+        "lastModified" : "1436102517799",
+        "name" : "C. elegans connectome",
+        "status" : "COMPLETED"
+      } ],
+  "geppettoModel" : { "id" : 6,
+      "type" : "GEPPETTO_PROJECT",
+      "url" : "/projects/cElegansConnectome/GeppettoModel.xmi"
+    },
+  "id" : 16,
+  "name" : "C. elegans multi-compartment connectome"
 }