Changed a number of variables (riset to group, db to dataset)

Put most of the code for cisLRS and transLRS searches into the class
CisTransLrsSearch (might change this name to something else later)

Simplified escape code for searches in do_search.py

Got search_results working again after some changes

1 files changed, 13 insertions, 13 deletions

diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index ff1db0e8..a3537c87 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -47,7 +47,7 @@ from utility import webqtlUtil
 class webqtlFormData(object):
     'Represents data from a WebQTL form page, needed to generate the next page'
 
-    attrs = ('formID','RISet','genotype','samplelist','allsamplelist', 'display_variance'
+    attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance'
                 'suggestive','significance','submitID','identification', 'enablevariance',
                 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
 
@@ -104,11 +104,11 @@ class webqtlFormData(object):
         self.ppolar = None
         self.mpolar = None
 
-        print("[yellow] self.RISet is:", self.RISet)
-        if self.RISet:
+        print("[yellow] self.group is:", self.group)
+        if self.group:
             #try:
             #    # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
-            _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet]
+            _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
             #except:
             #    f1 = f12 = self.mpolar = self.ppolar = None
 
@@ -129,8 +129,8 @@ class webqtlFormData(object):
         #self.readGenotype()
         #self.readData()
 
-        if self.RISet == 'BXD300':
-            self.RISet = 'BXD'
+        if self.group == 'BXD300':
+            self.group = 'BXD'
 
 
     def __getitem__(self, key):
@@ -153,17 +153,17 @@ class webqtlFormData(object):
 
     def readGenotype(self):
         '''read genotype from .geno file'''
-        if self.RISet == 'BXD300':
-            self.RISet = 'BXD'
+        if self.group == 'BXD300':
+            self.group = 'BXD'
 
-        assert self.RISet, "self.RISet needs to be set"
+        assert self.group, "self.group needs to be set"
 
         #genotype_1 is Dataset Object without parents and f1
         #genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
         self.genotype_1 = reaper.Dataset()
 
-        full_filename = os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')
+        full_filename = os.path.join(webqtlConfig.GENODIR, self.group + '.geno')
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
         full_filename = str(full_filename)
@@ -173,12 +173,12 @@ class webqtlFormData(object):
 
         try:
             # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
-            _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet]
+            _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group]
         except KeyError:
             _f1 = _f12 = _mat = _pat = None
 
         self.genotype_2 = self.genotype_1
-        if self.genotype_1.type == "riset" and _mat and _pat:
+        if self.genotype_1.type == "group" and _mat and _pat:
             self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat)       #, F1=_f1)
 
         #determine default genotype object
@@ -333,7 +333,7 @@ class webqtlFormData(object):
 
     def Sample(self):
         'Create some dummy data for testing'
-        self.RISet = 'BXD'
+        self.group = 'BXD'
         self.incparentsf1 = 'on'
         #self.display = 9.2
         #self.significance = 16.1