From 8bd404246b83f46f34c9b162c39c2dfc6ab39049 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 28 Sep 2012 16:56:42 -0500
Subject: Removed show_trait_page.py and moved relevant code over to
 DataEditingPage.py (though the user security stuff still needs to be moved
 over)

---
 wqflask/base/webqtlFormData.py                |  1 +
 wqflask/wqflask/show_trait/DataEditingPage.py | 44 +++++++++++++++++++++++++--
 wqflask/wqflask/views.py                      |  6 ++--
 3 files changed, 46 insertions(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 63263895..710c9f53 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -43,6 +43,7 @@ from utility import webqtlUtil
 
 
 
+
 class webqtlFormData:
     'Represents data from a WebQTL form page, needed to generate the next page'
     
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index 92d0feaf..12e816f8 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -20,13 +20,29 @@ from basicStatistics import BasicStatisticsFunctions
 
 from pprint import pformat as pf
 
+###############################################
+#
+# Todo: Put in security to ensure that user has permission to access confidential data sets
+# And add i.p.limiting as necessary
+#
+##############################################
+
+
+
 class DataEditingPage(templatePage):
 
-    def __init__(self, fd, this_trait=None):
+    def __init__(self, fd):
+        self.fd = fd
 
         templatePage.__init__(self, fd)
         assert self.openMysql(), "No datbase!"
         
+        this_trait = self.get_this_trait()
+        
+        ##read genotype file
+        fd.RISet = this_trait.riset
+        fd.readGenotype()        
+        
         if not fd.genotype:
             fd.readData(incf1=1)
 
@@ -43,7 +59,6 @@ class DataEditingPage(templatePage):
             else:
                 fmID='dataEditing'
 
-
         # Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery
         hddn = OrderedDict(
                 FormID = fmID,
@@ -149,6 +164,31 @@ class DataEditingPage(templatePage):
         self.js_data = dict(sample_groups = self.sample_group_types)
 
 
+    def get_this_trait(self):
+        # When is traitInfos used?
+        #if traitInfos:
+        #    database, ProbeSetID, CellID = traitInfos
+        #else:
+        database = self.fd['database']
+        probe_set_id = self.fd['ProbeSetID']
+        cell_id = self.fd.get('CellID')        
+
+        this_trait =  webqtlTrait(db=database, name=probe_set_id, cellid=cell_id, cursor=self.cursor)
+    
+        ##identification, etc.
+        self.fd.identification = '%s : %s' % (this_trait.db.shortname, probe_set_id)
+        this_trait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
+                &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, probe_set_id, self.fd['RISet'])
+
+        if cell_id:
+            self.fd.identification = '%s/%s'%(self.fd.identification, cell_id)
+            this_trait.returnURL = '%s&CellID=%s' % (this_trait.returnURL, cell_id)
+
+        this_trait.retrieveInfo()
+        this_trait.retrieveData()
+        return this_trait
+    
+
     def dispTraitInformation(self, fd, title1Body, hddn, this_trait):
 
         _Species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 0befb74a..bc80a1e6 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -10,7 +10,7 @@ from wqflask import app
 from flask import render_template, request
 
 from wqflask import search_results
-from wqflask.show_trait import show_trait_page
+from wqflask.show_trait import DataEditingPage
 from wqflask.correlation import CorrelationPage
 
 from wqflask.dataSharing import SharingInfo, SharingInfoPage
@@ -75,8 +75,8 @@ def whats_new():
 def show_trait():
     # Here it's currently too complicated not to use an fd that is a webqtlFormData
     fd = webqtlFormData.webqtlFormData(request.args)
-    template_vars = show_trait_page.ShowTraitPage(fd)
-    
+    #template_vars = show_trait_page.ShowTraitPage(fd)
+    template_vars = DataEditingPage.DataEditingPage(fd)
     template_vars.js_data = json.dumps(template_vars.js_data)
     
     print("show_trait template_vars:", pf(template_vars.__dict__))
-- 
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