Adding stub display templates for all 3 analysis tools

7 files changed, 104 insertions, 5 deletions

diff --git a/wqflask/wqflask/auwerx/ephewas.py b/wqflask/wqflask/auwerx/ephewas.py
new file mode 100644
index 00000000..edfb2801
--- /dev/null
+++ b/wqflask/wqflask/auwerx/ephewas.py
@@ -0,0 +1,40 @@
+# PheWAS analysis for GN2
+# Author / Maintainer: Li Hao & Danny Arends <Danny.Arends@gmail.com>
+import sys
+from numpy import *
+import scipy as sp                            # SciPy
+import rpy2.robjects as ro                    # R Objects
+import rpy2.rinterface as ri
+
+from base.webqtlConfig import GENERATED_IMAGE_DIR
+from utility import webqtlUtil                # Random number for the image
+from utility import genofile_parser           # genofile_parser
+
+import base64
+import array
+import csv
+import itertools
+
+from base import data_set
+from base import trait as TRAIT
+
+from utility import helper_functions
+from utility.tools import locate
+
+from rpy2.robjects.packages import importr
+utils = importr("utils")
+
+class EPheWAS(object):
+    def __init__(self):
+        print("Initialization of ePheWAS")
+        print("Initialization of ePheWAS done !")
+
+    def run_analysis(self, requestform):
+        print("Starting ePheWAS analysis on dataset")
+        print("Initialization of ePheWAS done !")
+
+    def process_results(self, results):
+        print("Processing ePheWAS output")
+        template_vars = {}
+        return(dict(template_vars))
+
diff --git a/wqflask/wqflask/auwerx/mediation.py b/wqflask/wqflask/auwerx/mediation.py
new file mode 100644
index 00000000..48d02dc2
--- /dev/null
+++ b/wqflask/wqflask/auwerx/mediation.py
@@ -0,0 +1,40 @@
+# PheWAS analysis for GN2
+# Author / Maintainer: Li Hao & Danny Arends <Danny.Arends@gmail.com>
+import sys
+from numpy import *
+import scipy as sp                            # SciPy
+import rpy2.robjects as ro                    # R Objects
+import rpy2.rinterface as ri
+
+from base.webqtlConfig import GENERATED_IMAGE_DIR
+from utility import webqtlUtil                # Random number for the image
+from utility import genofile_parser           # genofile_parser
+
+import base64
+import array
+import csv
+import itertools
+
+from base import data_set
+from base import trait as TRAIT
+
+from utility import helper_functions
+from utility.tools import locate
+
+from rpy2.robjects.packages import importr
+utils = importr("utils")
+
+class Mediation(object):
+    def __init__(self):
+        print("Initialization of Mediation")
+        print("Initialization of Mediation done !")
+
+    def run_analysis(self, requestform):
+        print("Starting Mediation analysis on dataset")
+        print("Initialization of Mediation done !")
+
+    def process_results(self, results):
+        print("Processing Mediation output")
+        template_vars = {}
+        return(dict(template_vars))
+
diff --git a/wqflask/wqflask/phewas/phewas.py b/wqflask/wqflask/auwerx/phewas.py
index 399e056c..399e056c 100644
--- a/wqflask/wqflask/phewas/phewas.py
+++ b/wqflask/wqflask/auwerx/phewas.py
diff --git a/wqflask/wqflask/templates/ephewas_analysis.html b/wqflask/wqflask/templates/ephewas_analysis.html
new file mode 100644
index 00000000..d5e71fa7
--- /dev/null
+++ b/wqflask/wqflask/templates/ephewas_analysis.html
@@ -0,0 +1,9 @@
+{% extends "base.html" %}
+{% block title %}ePheWAS analysis{% endblock %}
+
+{% block content %} <!-- Start of body -->
+<div class="container">
+  <h1>ePheWAS analysis results</h1>
+  YAY ! We have our own route
+</div>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/mediation_analysis.html b/wqflask/wqflask/templates/mediation_analysis.html
new file mode 100644
index 00000000..ee5a5016
--- /dev/null
+++ b/wqflask/wqflask/templates/mediation_analysis.html
@@ -0,0 +1,9 @@
+{% extends "base.html" %}
+{% block title %}Mediation analysis{% endblock %}
+
+{% block content %} <!-- Start of body -->
+<div class="container">
+  <h1>Mediation analysis results</h1>
+  YAY ! We have our own route
+</div>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/phewas_analysis.html b/wqflask/wqflask/templates/phewas_analysis.html
index ac163b43..2b04d85b 100644
--- a/wqflask/wqflask/templates/phewas_analysis.html
+++ b/wqflask/wqflask/templates/phewas_analysis.html
@@ -1,8 +1,9 @@
 {% extends "base.html" %}
-{% block title %}CTL analysis{% endblock %}
+{% block title %}PheWAS analysis{% endblock %}
 
 {% block content %} <!-- Start of body -->
 <div class="container">
+  <h1>PheWAS analysis results</h1>
   YAY ! We have our own route
 </div>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_PheWAS_tools.html b/wqflask/wqflask/templates/show_trait_PheWAS_tools.html
index ee4c5f5a..d8193652 100644
--- a/wqflask/wqflask/templates/show_trait_PheWAS_tools.html
+++ b/wqflask/wqflask/templates/show_trait_PheWAS_tools.html
@@ -40,7 +40,7 @@
                 </div>
                 <div class="form-group">
                   <div style="padding-left:15px;" class="controls">
-                    <button id="phewas_compute" class="btn btn-primary submit_special" data-url="/phewas" title="Compute PheWAS">
+                    <button id="phewas_compute" class="btn btn-primary submit_special" title="Compute PheWAS">
                       <i class="icon-ok-circle icon-white"></i> Compute
                     </button>
                   </div>
@@ -59,7 +59,7 @@
                 </div>
                 <div class="form-group">
                   <div style="padding-left:15px;" class="controls">
-                    <button id="phewas_compute" class="btn submit_special btn-primary" data-url="/phewas" title="Compute PheWAS">
+                    <button id="ephewas_compute" class="btn submit_special btn-primary" title="Compute ePheWAS">
                       <i class="icon-ok-circle icon-white"></i> Compute
                     </button>
                   </div>
@@ -78,13 +78,13 @@
                 </div>
                 <div class="form-group">
                   <div style="padding-left:15px;" class="controls">
-                    <button id="phewas_compute" class="btn submit_special btn-primary" data-url="/phewas" title="Compute PheWAS">
+                    <button id="mediation_compute" class="btn submit_special btn-primary" title="Run mediation analysis">
                       <i class="icon-ok-circle icon-white"></i> Compute
                     </button>
                   </div>
                 </div>
             </div>
-          </div> <!-- end of the ePheWAS tab -->
+          </div> <!-- end of the Mediation tab -->
 
         </div>
       </ul>