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-rw-r--r--misc/find.txt1
-rw-r--r--misc/python_stuff.txt1
-rwxr-xr-xwqflask/base/webqtlCaseData.py69
-rwxr-xr-xwqflask/base/webqtlTrait.py52
-rwxr-xr-xwqflask/utility/webqtlUtil.py7
-rwxr-xr-xwqflask/wqflask/show_trait/DataEditingPage.py276
-rw-r--r--wqflask/wqflask/show_trait/show_trait_page.py27
-rw-r--r--wqflask/wqflask/templates/trait_data_and_analysis.html24
8 files changed, 261 insertions, 196 deletions
diff --git a/misc/find.txt b/misc/find.txt
new file mode 100644
index 00000000..5c792d80
--- /dev/null
+++ b/misc/find.txt
@@ -0,0 +1 @@
+find | grep _____
diff --git a/misc/python_stuff.txt b/misc/python_stuff.txt
new file mode 100644
index 00000000..f36fe338
--- /dev/null
+++ b/misc/python_stuff.txt
@@ -0,0 +1 @@
+Classes should always inherit "object" \ No newline at end of file
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index f68354be..7805df06 100755
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -24,28 +24,59 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-class webqtlCaseData:
- """
- one case data in one trait
- """
+print("Mr. Mojo Risin 2")
- val = None #Trait Value
- var = None #Trait Variance
- N = None #Number of individuals
+class webqtlCaseData(object):
+ """one case data in one trait
+
+ """
- def __init__(self, val=val, var=var, N=N):
- self.val = val
- self.var = var
- self.N = N
+ def __init__(self, name, value=None, variance=None, num_cases=None):
+ self.name = name
+ self.value = value # Trait Value
+ self.variance = variance # Trait Variance
+ self.num_cases = num_cases # Number of individuals/cases
+ self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word)
- def __str__(self):
+ def __repr__(self):
str = ""
- if self.val != None:
- str += "value=%2.3f" % self.val
- if self.var != None:
- str += " variance=%2.3f" % self.var
- if self.N != None:
- str += " ndata=%d" % self.N
+ if self.value != None:
+ str += "value=%2.3f" % self.value
+ if self.variance != None:
+ str += " variance=%2.3f" % self.variance
+ if self.num_cases != None:
+ str += " ndata=%d" % self.num_cases
return str
+
+ @property
+ def display_value(self):
+ if self.value:
+ return "%2.3f" % self.value
+ else:
+ return "x"
+
+ @property
+ def display_variance(self):
+ if self.variance:
+ return "%2.3f" % self.variance
+ else:
+ return "x"
+
+
+ #try:
+ # traitVar = thisvar
+ # dispVar = "%2.3f" % thisvar
+ #except:
+ # traitVar = ''
+ # dispVar = 'x'
+
+ #try:
+ # traitVal = thisval
+ # dispVal = "%2.3f" % thisval
+ #except:
+ # traitVal = ''
+ # dispVal = 'x'
+
- __repr__ = __str__
+ #def this_val_full(self):
+ # strain_name = \ No newline at end of file
diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 23b98238..337493ef 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -225,7 +225,10 @@ class webqtlTrait:
- def retrieveData(self, strainlist=[]):
+ def retrieveData(self, strainlist=None):
+
+ if strainlist == None:
+ strainlist = []
assert self.db and self.cursor
if self.db.type == 'Temp':
@@ -328,32 +331,33 @@ class webqtlTrait:
self.cursor.execute(query)
results = self.cursor.fetchall()
self.data.clear()
+
if results:
self.mysqlid = results[0][-1]
- if strainlist:
- for item in results:
- if item[0] in strainlist:
- val = item[1]
- if val != None:
- var = item[2]
- ndata = None
- if self.db.type in ('Publish', 'Temp'):
- ndata = item[3]
- self.data[item[0]] = webqtlCaseData(val, var, ndata)
+ #if strainlist:
+ for item in results:
+ #name, value, variance, num_cases = item
+ if not strainlist or (strainlist and name in strainlist):
+ #if value != None:
+ # num_cases = None
+ # if self.db.type in ('Publish', 'Temp'):
+ # ndata = item[3]
+ name = item[0]
+ self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
#end for
- else:
- for item in results:
- val = item[1]
- if val != None:
- var = item[2]
- ndata = None
- if self.db.type in ('Publish', 'Temp'):
- ndata = item[3]
- self.data[item[0]] = webqtlCaseData(val, var, ndata)
- #end for
- #end if
- else:
- pass
+ # else:
+ # for item in results:
+ # val = item[1]
+ # if val != None:
+ # var = item[2]
+ # ndata = None
+ # if self.db.type in ('Publish', 'Temp'):
+ # ndata = item[3]
+ # self.data[item[0]] = webqtlCaseData(val, var, ndata)
+ # #end for
+ # #end if
+ #else:
+ # pass
def keys(self):
return self.__dict__.keys()
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 6409e781..99451e33 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -252,7 +252,12 @@ def FloatList2String(lst):
return ""
def ListNotNull(lst):
- 'Determine if the elements in a list are all null'
+ '''Obsolete - Use built in function any (or all or whatever)
+
+
+ Determine if the elements in a list are all null
+
+ '''
for item in lst:
if item is not None:
return 1
diff --git a/wqflask/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index f9133f27..43f05f14 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -11,6 +11,7 @@ import yaml
from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
+from base import webqtlCaseData
from utility import webqtlUtil, Plot
from base.webqtlTrait import webqtlTrait
from dbFunction import webqtlDatabaseFunction
@@ -172,17 +173,17 @@ class DataEditingPage(templatePage):
if thisTrait == None:
thisTrait = webqtlTrait(data=fd.allTraitData, db=None)
- # Variance submit page only
- if fd.enablevariance and not varianceDataPage:
- pass
- #title2Body.append("Click the next button to go to the variance submission form.",
- # HT.Center(next,reset))
- else:
- pass
- # We'll get this part working later
- print("Calling dispBasicStatistics")
- self.dispBasicStatistics(fd, thisTrait)
- #self.dispMappingTools(fd, title4Body, thisTrait)
+ ## Variance submit page only
+ #if fd.enablevariance and not varianceDataPage:
+ # pass
+ # #title2Body.append("Click the next button to go to the variance submission form.",
+ # # HT.Center(next,reset))
+ #else:
+ # pass
+ # # We'll get this part working later
+ # print("Calling dispBasicStatistics")
+ # self.dispBasicStatistics(fd, thisTrait)
+ # #self.dispMappingTools(fd, title4Body, thisTrait)
#############################
## Trait Value Table
@@ -892,13 +893,13 @@ class DataEditingPage(templatePage):
for strain in thisTrait.data.keys():
strainName = strain.replace("_2nd_", "")
if strain not in strainlist:
- if (thisTrait.data[strainName].val != None):
+ if thisTrait.data[strainName].value != None:
if strain.find('F1') < 0:
specialStrains.append(strain)
- if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)):
+ if (thisTrait.data[strainName].value != None) and (strain not in (fd.f1list + fd.parlist)):
other_strains.append(strain) #XZ: at current stage, other_strains doesn't include parent strains and F1 strains of primary group
else:
- if (thisTrait.data[strainName].val != None) and (strain not in (fd.f1list + fd.parlist)):
+ if (thisTrait.data[strainName].value != None) and (strain not in (fd.f1list + fd.parlist)):
primary_strains.append(strain) #XZ: at current stage, the primary_strains is the same as fd.strainlist / ZS: I tried defining primary_strains as fd.strainlist instead, but in some cases it ended up including the parent strains (1436869_at BXD)
if len(other_strains) > 3:
@@ -941,41 +942,58 @@ class DataEditingPage(templatePage):
vals3 = []
#Using all strains/cases for values
- for i, strainNameOrig in enumerate(all_strains):
+ #for strain_type in (all_strains, primary_strains, other_strains):
+ for strainNameOrig in all_strains:
strainName = strainNameOrig.replace("_2nd_", "")
- try:
- thisval = thisTrait.data[strainName].val
- thisvar = thisTrait.data[strainName].var
- thisValFull = [strainName, thisval, thisvar]
- except:
- continue
+ #try:
+ print("* type of thisTrait:", type(thisTrait))
+ print(" name:", thisTrait.__class__.__name__)
+ print(" thisTrait:", thisTrait)
+ print(" type of thisTrait.data[strainName]:", type(thisTrait.data[strainName]))
+ print(" name:", thisTrait.data[strainName].__class__.__name__)
+ print(" thisTrait.data[strainName]:", thisTrait.data[strainName])
+ thisval = thisTrait.data[strainName].value
+ print(" thisval:", thisval)
+ thisvar = thisTrait.data[strainName].variance
+ print(" thisvar:", thisvar)
+ thisValFull = [strainName, thisval, thisvar]
+ print(" thisValFull:", thisValFull)
+ #except:
+ # continue
vals1.append(thisValFull)
+
+
+ #vals1 = [[strainNameOrig.replace("_2nd_", ""),
+ # thisTrait.data[strainName].val,
+ # thisTrait.data[strainName].var]
+ # for strainNameOrig in all_strains]]
+ #
#Using just the RISet strain
- for i, strainNameOrig in enumerate(primary_strains):
+ for strainNameOrig in primary_strains:
strainName = strainNameOrig.replace("_2nd_", "")
- try:
- thisval = thisTrait.data[strainName].val
- thisvar = thisTrait.data[strainName].var
- thisValFull = [strainName,thisval,thisvar]
- except:
- continue
+ #try:
+ thisval = thisTrait.data[strainName].value
+ thisvar = thisTrait.data[strainName].variance
+ thisValFull = [strainName,thisval,thisvar]
+ #except:
+ # continue
vals2.append(thisValFull)
#Using all non-RISet strains only
- for i, strainNameOrig in enumerate(other_strains):
+ for strainNameOrig in other_strains:
strainName = strainNameOrig.replace("_2nd_", "")
- try:
- thisval = thisTrait.data[strainName].val
- thisvar = thisTrait.data[strainName].var
- thisValFull = [strainName,thisval,thisvar]
- except:
- continue
+ #try:
+ thisval = thisTrait.data[strainName].value
+ thisvar = thisTrait.data[strainName].variance
+ thisValFull = [strainName,thisval,thisvar]
+ #except:
+ # continue
vals3.append(thisValFull)
@@ -985,15 +1003,15 @@ class DataEditingPage(templatePage):
vals = []
#Using all strains/cases for values
- for i, strainNameOrig in enumerate(all_strains):
+ for strainNameOrig in all_strains:
strainName = strainNameOrig.replace("_2nd_", "")
- try:
- thisval = thisTrait.data[strainName].val
- thisvar = thisTrait.data[strainName].var
- thisValFull = [strainName,thisval,thisvar]
- except:
- continue
+ #try:
+ thisval = thisTrait.data[strainName].value
+ thisvar = thisTrait.data[strainName].variance
+ thisValFull = [strainName,thisval,thisvar]
+ #except:
+ # continue
vals.append(thisValFull)
@@ -1344,24 +1362,26 @@ class DataEditingPage(templatePage):
# updated by NL 5-28-2010
# Interval Mapping
chrMenu = HT.Select(name='chromosomes1')
- chrMenu.append(tuple(["All",-1]))
+ chrMenu.append(("All",-1))
for i in range(len(fd.genotype)):
- if len(fd.genotype[i]) > 1:
- chrMenu.append(tuple([fd.genotype[i].name,i]))
+ if len(fd.genotype[i]) > 1:
+ chrMenu.append((fd.genotype[i].name, i))
#Menu for Composite Interval Mapping
chrMenu2 = HT.Select(name='chromosomes2')
- chrMenu2.append(tuple(["All",-1]))
+ chrMenu2.append(("All",-1))
for i in range(len(fd.genotype)):
- if len(fd.genotype[i]) > 1:
- chrMenu2.append(tuple([fd.genotype[i].name,i]))
+ if len(fd.genotype[i]) > 1:
+ chrMenu2.append((fd.genotype[i].name, i))
if fd.genotype.Mbmap:
scaleText = HT.Span("Mapping Scale:", Class="ffl fwb fs12")
- scaleMenu1 = HT.Select(name='scale1', onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)")
+ scaleMenu1 = HT.Select(name='scale1',
+ onChange="checkUncheck(window.document.dataInput.scale1.value, window.document.dataInput.permCheck1, window.document.dataInput.bootCheck1)")
scaleMenu1.append(("Megabase",'physic'))
scaleMenu1.append(("Centimorgan",'morgan'))
- scaleMenu2 = HT.Select(name='scale2', onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)")
+ scaleMenu2 = HT.Select(name='scale2',
+ onChange="checkUncheck(window.document.dataInput.scale2.value, window.document.dataInput.permCheck2, window.document.dataInput.bootCheck2)")
scaleMenu2.append(("Megabase",'physic'))
scaleMenu2.append(("Centimorgan",'morgan'))
@@ -1521,7 +1541,7 @@ class DataEditingPage(templatePage):
submitTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%", Class="target2")
- if mappingMethodId != None:
+ if not mappingMethodId:
if int(mappingMethodId) == 1:
submitTable.append(mapping_row)
submitTable.append(mapping_script)
@@ -1567,17 +1587,6 @@ class DataEditingPage(templatePage):
title4Body.append(submitTable)
- def natural_sort(strain_list):
-
- sorted = []
- for strain in strain_list:
- try:
- strain = int(strain)
- try: sorted[-1] = sorted[-1] * 10 + strain
- except: sorted.append(strain)
- except:
- sorted.append(strain)
- return sorted
##########################################
## Function to display trait tables
@@ -1727,8 +1736,9 @@ class DataEditingPage(templatePage):
attribute_names=attribute_names,
strains='other')
- if other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0])) \
- or (fd.f1list and thisTrait.data.has_key(fd.f1list[1])):
+ #TODO: Figure out why this if statement is written this way - Zach
+ if (other_strains or (fd.f1list and thisTrait.data.has_key(fd.f1list[0]))
+ or (fd.f1list and thisTrait.data.has_key(fd.f1list[1]))):
print("hjs")
fd.allstrainlist = allstrainlist_neworder
@@ -1738,85 +1748,93 @@ class DataEditingPage(templatePage):
def addTrait2Table(self, fd, varianceDataPage, strainlist, mainForm, thisTrait,
- other_strainsExist=None, attribute_ids=[],
- attribute_names=[], strains='primary'):
+ other_strainsExist=None, attribute_ids=None,
+ attribute_names=None, strains='primary'):
+
+ if attribute_ids == None:
+ attribute_ids = []
+
+ if attribute_names == None:
+ attribute_names = []
+
#XZ, Aug 23, 2010: I commented the code related to the display of animal case
#strainInfo = thisTrait.has_key('strainInfo') and thisTrait.strainInfo
print("in addTrait2Table")
table_body = []
vals = []
- for i, strainNameOrig in enumerate(strainlist):
- strainName = strainNameOrig.replace("_2nd_", "")
-
- try:
- thisval = thisTrait.data[strainName].val
- thisvar = thisTrait.data[strainName].var
- thisValFull = [strainName,thisval,thisvar]
- except:
- continue
-
- vals.append(thisValFull)
- upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers.
+ #################### Only used to find upperBound and lowerBound
+ #for strainNameOrig in strainlist:
+ # strainName = strainNameOrig.replace("_2nd_", "")
+ # print("pen: %s - %s" % (strainNameOrig, strainName))
+ # thisval = thisTrait.data[strainName].value
+ # thisvar = thisTrait.data[strainName].variance
+ # thisValFull = [strainName, thisval, thisvar]
+ #
+ # vals.append(thisValFull)
+ #
+ #upperBound, lowerBound = Plot.findOutliers(vals) # ZS: Values greater than upperBound or less than lowerBound are considered outliers.
the_strains = []
- for i, strainNameOrig in enumerate(strainlist):
- strain = {}
- print("zyt - strainNameOrig:", strainNameOrig)
- trId = strainNameOrig
- #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)")
-
+ for counter, strainNameOrig in enumerate(strainlist, 1):
strainName = strainNameOrig.replace("_2nd_", "")
strainNameAdd = ''
if fd.RISet == 'AXBXA' and strainName in ('AXB18/19/20','AXB13/14','BXA8/17'):
strainNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
-
+
try:
- thisval, thisvar, thisNP = thisTrait.data[strainName].val, thisTrait.data[strainName].var, thisTrait.data[strainName].N
- if thisNP:
- mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden'))
- else:
- pass
- except:
- thisval = thisvar = 'x'
-
- try:
- traitVal = thisval
- dispVal = "%2.3f" % thisval
- except:
- traitVal = ''
- dispVal = 'x'
+ strain = thisTrait.data[strainName]
+ except KeyError:
+ print("No strain %s, let's create it now" % strainName)
+ strain = webqtlCaseData.webqtlCaseData(strainName)
+ print("zyt - strainNameOrig:", strainNameOrig)
+ #trId = strainNameOrig
+ #selectCheck = HT.Input(type="checkbox", name="selectCheck", value=trId, Class="checkbox", onClick="highlight(this)")
- strain['strain_name'] = strainName
- strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl')
+
+ #try:
+ # thisval, thisvar, thisNP = thisTrait.data[strainName].value, thisTrait.data[strainName].var, thisTrait.data[strainName].N
+ # if thisNP:
+ # mainForm.append(HT.Input(name='N'+strainName, value=thisNP, type='hidden'))
+ # else:
+ # pass
+ #except:
+ # thisval = thisvar = 'x'
- if varianceDataPage:
- try:
- traitVar = thisvar
- dispVar = "%2.3f" % thisvar
- except:
- traitVar = ''
- dispVar = 'x'
+ #thisval = thisTrait.data[strainName].value
+ #thisvar = thisTrait.data[strainName].variance
+ #thisTrait.data[strainName].num_cases
- if thisval == 'x':
- traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing"
+ #strain['strain_name'] = strainName
+ #strainNameDisp = HT.Span(strainName, Class='fs14 fwn ffl')
- #className = 'fs13 b1 c222 '
- #valueClassName = 'fs13 b1 c222 valueField '
- #rowClassName = 'novalue '
- else:
- if (thisval >= upperBound) or (thisval <= lowerBound):
- strain['outlier'] = "outlier" # We're going to use this as a class, so we want it to be a word
- #className = 'fs13 b1 c222 outlier '
- #valueClassName = 'fs13 b1 c222 valueField '
- #rowClassName = 'outlier'
- else:
- strain['outlier'] = "not_outlier"
- #className = 'fs13 b1 c222 '
- #valueClassName = 'fs13 b1 c222 valueField '
- #rowClassName = ' '
+ #if varianceDataPage:
+ #try:
+ # traitVar = thisvar
+ # dispVar = "%2.3f" % thisvar
+ #except:
+ # traitVar = ''
+ # dispVar = 'x'
+
+ #if thisval == 'x':
+ # traitVar = '' #ZS: Used to be 0, but it doesn't seem like a good idea for values of 0 to *always* be at the bottom when you sort; it makes more sense to put "nothing"
+ #
+ # #className = 'fs13 b1 c222 '
+ # #valueClassName = 'fs13 b1 c222 valueField '
+ # #rowClassName = 'novalue '
+ #else:
+ # if (thisval >= upperBound) or (thisval <= lowerBound):
+ # strain['outlier'] = "outlier" # We're going to use this as a class, so we want it to be a word
+ # #className = 'fs13 b1 c222 outlier '
+ # #valueClassName = 'fs13 b1 c222 valueField '
+ # #rowClassName = 'outlier'
+ # else:
+ # strain['outlier'] = "not_outlier"
+ # #className = 'fs13 b1 c222 '
+ # #valueClassName = 'fs13 b1 c222 valueField '
+ # #rowClassName = ' '
#
#if varianceDataPage:
# varClassName = valueClassName + str(traitVar)
@@ -1851,15 +1869,15 @@ class DataEditingPage(templatePage):
# # onChange= "javascript:this.form['V%s'].value=this.form['V%s'].value;" % (strainNameOrig.replace("/", ""), strainNameOrig.replace("/", "")), Class=varClassName)
if strains == 'primary':
- strain['the_id'] = "Primary_" + str(i+1)
+ strain.this_id = "Primary_" + str(counter)
#table_row = HT.TR(Id="Primary_"+str(i+1), Class=rowClassName)
else:
- strain['the_id'] = "Other_" + str(i+1)
+ strain.this_id = "Other_" + str(counter)
#table_row = HT.TR(Id="Other_"+str(i+1), Class=rowClassName)
- strain['value'] = traitVal
-
- strain['se'] = dispVar
+ #strain['value'] = traitVal
+ #
+ #strain['se'] = dispVar
#if varianceDataPage:
#table_row.append(HT.TD(str(i+1), selectCheck, width=45, align='right', Class=className))
#table_row.append(HT.TD(strainNameDisp, strainNameAdd, align='right', width=100, Class=className))
diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py
index b1f71e55..b42f5e8e 100644
--- a/wqflask/wqflask/show_trait/show_trait_page.py
+++ b/wqflask/wqflask/show_trait/show_trait_page.py
@@ -161,24 +161,25 @@ class ShowTraitPage(DataEditingPage):
thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID)
#retrieve trait information
- try:
- thisTrait.retrieveInfo()
- thisTrait.retrieveData()
- self.updMysql()
- self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip)
- self.openMysql()
- except Exception as why:
- print("Got an exception:", why)
- heading = "Retrieve Data"
- detail = ["The information you requested is not avaiable at this time."]
- self.error(heading=heading, detail=detail)
- return
+ #try:
+ thisTrait.retrieveInfo()
+ thisTrait.retrieveData()
+ self.updMysql()
+ self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip)
+ self.openMysql()
+ #except Exception as why:
+ # print("Got an exception:", why)
+ # heading = "Retrieve Data"
+ # detail = ["The information you requested is not avaiable at this time."]
+ # self.error(heading=heading, detail=detail)
+ # return
##read genotype file
fd.RISet = thisTrait.riset
fd.readGenotype()
- if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
+ #if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
+ if any([x.variance for x in thisTrait.data.values()]):
fd.displayVariance = 1
fd.varianceDispName = 'SE'
fd.formID = 'varianceChoice'
diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html
index 4bf06d45..94ba0aad 100644
--- a/wqflask/wqflask/templates/trait_data_and_analysis.html
+++ b/wqflask/wqflask/templates/trait_data_and_analysis.html
@@ -8,7 +8,7 @@
<table width="100%" cellspacing="0" cellpadding="5">
<tr>
<td valign="top" width="100%" bgcolor="#FAFAFA">
- <form method="post" action="/webqtl/main.py" name="dataInput">
+ <form method="post" action="/webqtl/main.py" name="dataInput"></form>
{# <input type="hidden" name="isSE" value="yes">
<input type="hidden" name="permCheck">
<input type="hidden" name="otherStrainVals" value="_">
@@ -3059,7 +3059,7 @@
</div><br>
{% for strain_type in (primary_strains, other_strains) %}
- <div id="{{ strain_type[0]['the_id'].lower().partition('_')[0] }}"> {# Slightly tortuous, but best way to get the id we need #}
+ <div id="{{ strain_type[0]['this_id'].lower().partition('_')[0] }}"> {# Slightly tortuous, but best way to get the id we need #}
<table class="not_tablesorter" {# Todo: Turn tablesorter back on #}
id="{{ 'sortable%i' % (loop.index) }}"
cellpadding="0" cellspacing="0">
@@ -3076,20 +3076,20 @@
</tr>
{% for strain in strain_type %}
- <tr class="{{ strain.outlier }} value_se" id="{{ strain.the_id }}">
+ <tr class="{{ strain.outlier }} value_se" id="{{ strain.this_id }}">
<td class="fs13 b1 c222" align="right" width="45">
{{ loop.index }}
- <input type="checkbox" name="selectCheck" class="checkbox edit_strain_checkbox" value="{{ strain.strain_name }}" checked="checked">
+ <input type="checkbox" name="selectCheck" class="checkbox edit_strain_checkbox" value="{{ strain.name }}" checked="checked">
</td>
<td class="fs13 b1 c222" align="right" width="100">
- <span class="fs14 fwn ffl edit_strain_strain_name">{{ strain.strain_name }}</span>
+ <span class="fs14 fwn ffl edit_strain_strain_name">{{ strain.name }}</span>
</td>
{# Todo: Add IDs #}
<td class="fs13 b1 c222" align="right" width="70">
- <input type="text" name="{{ strain.strain_name }}" class="fs13 b1 c222 edit_strain_value valueField"
- value="{{ strain.value }}" size="8" maxlength="8"
+ <input type="text" name="{{ strain.name }}" class="fs13 b1 c222 edit_strain_value valueField"
+ value="{{ strain.display_value }}" size="8" maxlength="8"
style="text-align:right; background-color:#FFFFFF;">
</td>
@@ -3099,8 +3099,8 @@
{# Todo: Add IDs #}
<td class="fs13 b1 c222" align="right" width="80">
- <input type="text" name=""{{ 'V' + strain.strain_name}}" class="fs13 b1 c222 valueField edit_strain_se"
- value="{{ strain.se }}"
+ <input type="text" name=""{{ 'V' + strain.name}}" class="fs13 b1 c222 valueField edit_strain_se"
+ value="{{ strain.display_variance }}"
size="8" maxlength="8" style="text-align:right"></td>
</tr>
{% endfor %}
@@ -3133,4 +3133,8 @@
<!-- End of body -->
- {% endblock %}
+
+
+
+
+ {% endblock %}