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authorZachary Sloan2012-09-12 18:22:45 -0500
committerZachary Sloan2012-09-12 18:22:45 -0500
commitf1d7725c5f7529c5f587bab4ea89d3467b903ddb (patch)
tree899dd0c7fe717412bc91b93661fd0498fd227e2f /wqflask/base
parente7e3117695ef86a28df96cf32bfb66f6da2bc404 (diff)
downloadgenenetwork2-f1d7725c5f7529c5f587bab4ea89d3467b903ddb.tar.gz
Worked towards correctly passing form data to correlation page and addressed various bugs that arose while doing so
Diffstat (limited to 'wqflask/base')
-rwxr-xr-xwqflask/base/webqtlFormData.py121
1 files changed, 65 insertions, 56 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index a9e3b7d4..177c72a2 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -60,17 +60,12 @@ class webqtlFormData:
print("in webqtlFormData start_vars are:", pf(start_vars))
for item in webqtlFormData.attrs:
self.__dict__[item] = None
- #self.__dict__.update(start_vars)
+
for item in start_vars:
self.__dict__[item] = start_vars[item]
- print(" Now self.dict is:", pf(self.__dict__))
- #for item in self.attrs:
- # if getattr(self, item, None):
- # print("Setting item %s to None" % (item,))
- # self.attrs[item] = None
- # else:
- # self.attrs[item] = self.attrs[item].strip()
+ #print(" Now self.dict is:", pf(self.__dict__))
+ #Todo: This can't be good below...rework
try:
self.remote_ip = req.connection.remote_ip
except:
@@ -151,23 +146,32 @@ class webqtlFormData:
def readGenotype(self):
- 'read genotype from .geno file'
+ '''read genotype from .geno file'''
if self.RISet == 'BXD300':
self.RISet = 'BXD'
- else:
- pass
- assert self.RISet
+
+ assert self.RISet, "self.RISet 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()
- self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
+
+ full_filename = os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')
+
+ # reaper barfs on unicode filenames, so here we ensure it's a string
+ full_filename = str(full_filename)
+ self.genotype_1.read(full_filename)
+
+ print("Got to after read")
+
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet]
- except:
+ except KeyError:
_f1 = _f12 = _mat = _pat = None
- self.genotype_2 =self.genotype_1
+ self.genotype_2 = self.genotype_1
if self.genotype_1.type == "riset" and _mat and _pat:
self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1)
@@ -177,78 +181,83 @@ class webqtlFormData:
else:
self.incparentsf1 = 0
self.genotype = self.genotype_1
+
self.strainlist = list(self.genotype.prgy)
- self.f1list = self.parlist = []
+ self.f1list = []
+ self.parlist = []
+
if _f1 and _f12:
self.f1list = [_f1, _f12]
if _mat and _pat:
self.parlist = [_mat, _pat]
+
- def readData(self, strainlst=[], incf1=[]):
- 'read user input data or from trait data and analysis form'
+ def readData(self, strainlist, incf1=None):
+ '''read user input data or from trait data and analysis form'''
+
+ if incf1 == None:
+ incf1 = []
if not self.genotype:
self.readGenotype()
- if not strainlst:
+ if not strainlist:
if incf1:
- strainlst = self.f1list + self.strainlist
+ strainlist = self.f1list + self.strainlist
else:
- strainlst = self.strainlist
+ strainlist = self.strainlist
+ #print("before traitfiledata self.traitfile is:", pf(self.traitfile))
- traitfiledata = self.formdata.getfirst('traitfile')
- traitpastedata = self.formdata.getfirst('traitpaste')
- variancefiledata = self.formdata.getfirst('variancefile')
- variancepastedata = self.formdata.getfirst('variancepaste')
- Nfiledata = self.formdata.getfirst('Nfile')
+ traitfiledata = getattr(self, "traitfile", None)
+ traitpastedata = getattr(self, "traitpaste", None)
+ variancefiledata = getattr(self, "variancefile", None)
+ variancepastedata = getattr(self, "variancepaste", None)
+ Nfiledata = getattr(self, "Nfile", None)
+ #### Todo: Rewrite below when we get to someone submitting their own trait #####
if traitfiledata:
- tt = string.split(traitfiledata)
- vals = map(webqtlUtil.StringAsFloat, tt)
+ tt = traitfiledata.split()
+ values = map(webqtlUtil.StringAsFloat, tt)
elif traitpastedata:
- tt = string.split(traitpastedata)
- vals = map(webqtlUtil.StringAsFloat, tt)
+ tt = traitpastedata.split()
+ values = map(webqtlUtil.StringAsFloat, tt)
else:
- vals = map(self.FormDataAsFloat, strainlst)
-
- if len(vals) < len(strainlst):
- vals += [None]*(len(strainlst) - len(vals))
- elif len(vals) > len(strainlst):
- vals = vals[:len(strainlst)]
- else:
- pass
+ values = map(self.FormDataAsFloat, strainlist)
+ if len(values) < len(strainlist):
+ values += [None] * (len(strainlist) - len(values))
+ elif len(values) > len(strainlist):
+ values = values[:len(strainlist)]
+
if variancefiledata:
- tt = string.split(variancefiledata)
- vars = map(webqtlUtil.StringAsFloat, tt)
+ tt = variancefiledata.split()
+ variances = map(webqtlUtil.StringAsFloat, tt)
elif variancepastedata:
- tt = string.split(variancepastedata)
- vars = map(webqtlUtil.StringAsFloat, tt)
+ tt = variancepastedata.split()
+ variances = map(webqtlUtil.StringAsFloat, tt)
else:
- vars = map(self.FormVarianceAsFloat, strainlst)
+ variances = map(self.FormVarianceAsFloat, strainlist)
- if len(vars) < len(strainlst):
- vars += [None]*(len(strainlst) - len(vars))
- elif len(vars) > len(strainlst):
- vars = vars[:len(strainlst)]
- else:
- pass
+ if len(variances) < len(strainlist):
+ variances += [None]*(len(strainlist) - len(variances))
+ elif len(variances) > len(strainlist):
+ variances = variances[:len(strainlist)]
if Nfiledata:
tt = string.split(Nfiledata)
nstrains = map(webqtlUtil.IntAsFloat, tt)
- if len(nstrains) < len(strainlst):
- nstrains += [None]*(len(strainlst) - len(nstrains))
+ if len(nstrains) < len(strainlist):
+ nstrains += [None]*(len(strainlist) - len(nstrains))
else:
- nstrains = map(self.FormNAsFloat, strainlst)
+ nstrains = map(self.FormNAsFloat, strainlist)
- ##vals, vars, nstrains is obsolete
+ ##values, variances, nstrains is obsolete
self.allTraitData = {}
- for i, _strain in enumerate(strainlst):
- if vals[i] != None:
- self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i])
+ for i, _strain in enumerate(strainlist):
+ if values[i] != None:
+ self.allTraitData[_strain] = webqtlCaseData(values[i], variances[i], nstrains[i])