From 317eb5cfb23b3cb5979eb1eb516cacf086b09a44 Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Wed, 8 Feb 2017 09:31:38 +0100
Subject: Adding stub display templates for all 3 analysis tools

---
 wqflask/wqflask/auwerx/ephewas.py                  | 40 ++++++++++++++++++++++
 wqflask/wqflask/auwerx/mediation.py                | 40 ++++++++++++++++++++++
 wqflask/wqflask/auwerx/phewas.py                   | 40 ++++++++++++++++++++++
 wqflask/wqflask/phewas/phewas.py                   | 40 ----------------------
 wqflask/wqflask/templates/ephewas_analysis.html    |  9 +++++
 wqflask/wqflask/templates/mediation_analysis.html  |  9 +++++
 wqflask/wqflask/templates/phewas_analysis.html     |  3 +-
 .../wqflask/templates/show_trait_PheWAS_tools.html |  8 ++---
 8 files changed, 144 insertions(+), 45 deletions(-)
 create mode 100644 wqflask/wqflask/auwerx/ephewas.py
 create mode 100644 wqflask/wqflask/auwerx/mediation.py
 create mode 100644 wqflask/wqflask/auwerx/phewas.py
 delete mode 100644 wqflask/wqflask/phewas/phewas.py
 create mode 100644 wqflask/wqflask/templates/ephewas_analysis.html
 create mode 100644 wqflask/wqflask/templates/mediation_analysis.html

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/auwerx/phewas.py b/wqflask/wqflask/auwerx/phewas.py
new file mode 100644
index 00000000..399e056c
--- /dev/null
+++ b/wqflask/wqflask/auwerx/phewas.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 PheWAS(object):
+    def __init__(self):
+        print("Initialization of PheWAS")
+        print("Initialization of PheWAS done !")
+
+    def run_analysis(self, requestform):
+        print("Starting PheWAS analysis on dataset")
+        print("Initialization of PheWAS done !")
+
+    def process_results(self, results):
+        print("Processing PheWAS output")
+        template_vars = {}
+        return(dict(template_vars))
+
diff --git a/wqflask/wqflask/phewas/phewas.py b/wqflask/wqflask/phewas/phewas.py
deleted file mode 100644
index 399e056c..00000000
--- a/wqflask/wqflask/phewas/phewas.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# 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 PheWAS(object):
-    def __init__(self):
-        print("Initialization of PheWAS")
-        print("Initialization of PheWAS done !")
-
-    def run_analysis(self, requestform):
-        print("Starting PheWAS analysis on dataset")
-        print("Initialization of PheWAS done !")
-
-    def process_results(self, results):
-        print("Processing PheWAS output")
-        template_vars = {}
-        return(dict(template_vars))
-
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>
-- 
cgit v1.2.3