From a00aa60ad46e7e9e5531a1bbc04029c9ce27e6cc Mon Sep 17 00:00:00 2001
From: Asher <asher.pasha@utoronto.ca>
Date: Tue, 4 Oct 2016 19:00:37 -0400
Subject: [PATCH] The page loads now.

---
 app/data/heatMap/viewsMap.json                | 32 +++++++++----------
 app/data/molecule/AcidLetterMap.json          |  1 -
 .../Eplant.Views.MoleculeView3.js             |  4 +--
 app/scripts/src/Eplant.js                     |  5 +++
 araport-app.json                              |  3 ++
 lib/test-runner.js                            |  2 +-
 6 files changed, 27 insertions(+), 20 deletions(-)

diff --git a/app/data/heatMap/viewsMap.json b/app/data/heatMap/viewsMap.json
index 7d26198..261409c 100644
--- a/app/data/heatMap/viewsMap.json
+++ b/app/data/heatMap/viewsMap.json
@@ -1,62 +1,62 @@
 [  
    {  
       "name":"Plant",
-      "xmlurl":"data/plant/"
+      "xmlurl":"app/data/plant/"
    },
    {  
       "name":"Abiotic Stress",
-      "xmlurl":"data/experiment/efps/AbioticStress/"
+      "xmlurl":"app/data/experiment/efps/AbioticStress/"
    },
    {  
       "name":"Chemical",
-      "xmlurl":"data/experiment/efps/Chemical/"
+      "xmlurl":"app/data/experiment/efps/Chemical/"
    },
    {  
       "name":"Guard Cell Meristemoids",
-      "xmlurl":"data/experiment/efps/GuardCellMeristemoids/"
+      "xmlurl":"app/data/experiment/efps/GuardCellMeristemoids/"
    },
    {  
       "name":"Guard Cell Mutant And Wild Type Guard Cell ABA Response",
-      "xmlurl":"data/experiment/efps/GuardCellMutantAndWildTypeGuardCellABAResponse/"
+      "xmlurl":"app/data/experiment/efps/GuardCellMutantAndWildTypeGuardCellABAResponse/"
    },
    {  
       "name":"Guard Cell Suspension Cell ABA Response With ROS Scavenger",
-      "xmlurl":"data/experiment/efps/GuardCellSuspensionCellABAResponseWithROSScavenger/"
+      "xmlurl":"app/data/experiment/efps/GuardCellSuspensionCellABAResponseWithROSScavenger/"
    },
    {  
       "name":"Tissue Specific Guard And Mesophyll Cells",
-      "xmlurl":"data/experiment/efps/TissueSpecificGuardAndMesophyllCells/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificGuardAndMesophyllCells/"
    },
    {  
       "name":"Tissue Specific Pollen Germination",
-      "xmlurl":"data/experiment/efps/TissueSpecificPollenGermination/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificPollenGermination/"
    },
    {  
       "name":"Tissue Specific Root",
-      "xmlurl":"data/experiment/efps/TissueSpecificRoot/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificRoot/"
    },
    {  
       "name":"Tissue Specific Shoot Apical Meristem",
-      "xmlurl":"data/experiment/efps/TissueSpecificShootApicalMeristem/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificShootApicalMeristem/"
    },
    {  
       "name":"Tissue Specific Stem Epidermis",
-      "xmlurl":"data/experiment/efps/TissueSpecificStemEpidermis/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificStemEpidermis/"
    },
    {  
       "name":"Tissue Specific Stigma And Ovaries",
-      "xmlurl":"data/experiment/efps/TissueSpecificStigmaAndOvaries/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificStigmaAndOvaries/"
    },
    {  
       "name":"Tissue Specific Trichomes",
-      "xmlurl":"data/experiment/efps/TissueSpecificTrichomes/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificTrichomes/"
    },
    {  
       "name":"Tissue Specific Xylem And Cork",
-      "xmlurl":"data/experiment/efps/TissueSpecificXylemAndCork/"
+      "xmlurl":"app/data/experiment/efps/TissueSpecificXylemAndCork/"
    },
          {  
       "name":"Cell",
-      "xmlurl":"data/cell/"
+      "xmlurl":"app/data/cell/"
    }
-]
\ No newline at end of file
+]
diff --git a/app/data/molecule/AcidLetterMap.json b/app/data/molecule/AcidLetterMap.json
index 8270020..42812cb 100644
--- a/app/data/molecule/AcidLetterMap.json
+++ b/app/data/molecule/AcidLetterMap.json
@@ -15,7 +15,6 @@
 	"K":"Lys",
 	"M":"Met",
 	"F":"Phe",
-	"F":"Phe",
 	"P":"Pro",
 	"S":"Ser",
 	"T":"Thr",
diff --git a/app/scripts/src/Eplant.Views/MoleculeView/Eplant.Views.MoleculeView3.js b/app/scripts/src/Eplant.Views/MoleculeView/Eplant.Views.MoleculeView3.js
index b118cd7..bdc403b 100644
--- a/app/scripts/src/Eplant.Views/MoleculeView/Eplant.Views.MoleculeView3.js
+++ b/app/scripts/src/Eplant.Views/MoleculeView/Eplant.Views.MoleculeView3.js
@@ -148,8 +148,8 @@
 			Eplant.Views.MoleculeView.Params.htmlPage = data;
 		});
 
-		Eplant.Views.MoleculeView.Params.acidLetterMap = $.get(Eplant.Views.MoleculeView.Params.acidLetterMapUrl, function(data) {
-			Eplant.Views.MoleculeView.Params.acidLetterMap = JSON.parse( data );
+		Eplant.Views.MoleculeView.Params.acidLetterMap = $.getJSON(Eplant.Views.MoleculeView.Params.acidLetterMapUrl, function(data) {
+			Eplant.Views.MoleculeView.Params.acidLetterMap =  data;
 		});
 
 	};
diff --git a/app/scripts/src/Eplant.js b/app/scripts/src/Eplant.js
index 7163d14..1074d9c 100644
--- a/app/scripts/src/Eplant.js
+++ b/app/scripts/src/Eplant.js
@@ -1813,6 +1813,11 @@
 						
 						/* Add Species to ePlant */
 						Eplant.addSpecies(species);
+
+						/* Araport: Set Arabidopsis as active species */
+						if (n == 0) {
+							Eplant.setActiveSpecies(species);
+						}
 					}
 					
 					/* Set Species load status */
diff --git a/araport-app.json b/araport-app.json
index e500b54..bf832fc 100644
--- a/araport-app.json
+++ b/araport-app.json
@@ -167,5 +167,8 @@
     "scripts/js/jquery.mCustomScrollbar.css",
     "styles/eplant.css"
   ],
+  "tags": [
+    "arabidopsis", "eplant", "BAR"
+  ],
   "fullscreen": "require"
 }
diff --git a/lib/test-runner.js b/lib/test-runner.js
index 1ccd669..8af8756 100644
--- a/lib/test-runner.js
+++ b/lib/test-runner.js
@@ -93,6 +93,6 @@
   	  .fail(function( error ) {
   	    console.log( error );
   	  });
-  }, 5000);
+  }, 3000);
 
 })( window, jQuery, Agave );