def buildParamDict(fs, sessionfile):
params = {}
params["inputFile"] = fs.formdata.getvalue("inputFile", "")
params["progress"] = fs.formdata.getvalue("progress", "1")
params["filename"] = fs.formdata.getvalue("filename", "")
params["session"] = sessionfile
if type("1") != type(fs.formdata.getvalue("searchResult")):
params["searchResult"] = string.join(fs.formdata.getvalue("searchResult"),'\t')
else:
params["searchResult"] = fs.formdata.getvalue("searchResult")
params["riset"] = fs.formdata.getvalue("RISet", "")
#if params["filename"] == "":
# raise nGraphException("Required parameter filename missing")
#parameter determining whether export button returns an xgmml graph file or plain text file
params["exportFormat"] = fs.formdata.getvalue("exportFormat", "xgmml")
#parameter determining whether or not traits in the graph file are listed by their symbol or name
params["traitType"] = fs.formdata.getvalue("traitType", "symbol")
#parameter saying whether or not graph structure should be locked when you redraw the graph
params["lock"] = fs.formdata.getvalue("lock", "no")
#parameter saying what algorithm should be used to draw the graph
params["gType"] = fs.formdata.getvalue("gType", "none")
params["kValue"] = webqtlUtil.safeFloat(fs.formdata.getvalue("kValue", "0.5"), 0.5)
params["whichValue"] = webqtlUtil.safeInt(fs.formdata.getvalue("whichValue","0"),0)
# 1 inch = 2.54 cm
# 1 cm = 0.3937 inch
params["width"] = webqtlUtil.safeFloat(fs.formdata.getvalue("width", "40.0"), 40.0)
params["height"] = webqtlUtil.safeFloat(fs.formdata.getvalue("height", "40.0"), 40.0)
yesno = ["yes", "no"]
params["tune"] = webqtlUtil.safeString(fs.formdata.getvalue("tune", "yes"), yesno, "yes")
params["printIslands"] = webqtlUtil.safeInt(fs.formdata.getvalue("printIslands", "1"),1)
params["nodeshape"] = webqtlUtil.safeString(fs.formdata.getvalue("nodeshape","yes"), yesno, "yes")
params["nodelabel"] = webqtlUtil.safeString(fs.formdata.getvalue("nodelabel","no"), yesno, "no")
params["nfont"] = fs.formdata.getvalue("nfont","Arial")
params["nfontsize"] = webqtlUtil.safeFloat(fs.formdata.getvalue("nfontsize", "10.0"), 10.0)
params["splines"] = webqtlUtil.safeString(fs.formdata.getvalue("splines","yes"), yesno, "yes")
params["dispcorr"] = webqtlUtil.safeString(fs.formdata.getvalue("dispcorr","no"), yesno, "no")
params["cfont"] = fs.formdata.getvalue("cfont","Arial")
params["cfontsize"] = webqtlUtil.safeFloat(fs.formdata.getvalue("cfontsize", "10.0"), 10.0)
params["cPubName"] = fs.formdata.getvalue("cPubName","palegreen")
params["cMicName"] = fs.formdata.getvalue("cMicName","lightblue")
params["cGenName"] = fs.formdata.getvalue("cGenName","lightcoral")
params["cPubColor"] = fs.formdata.getvalue("cPubColor","98fb98")
params["cMicColor"] = fs.formdata.getvalue("cMicColor","add8e6")
params["cGenColor"] = fs.formdata.getvalue("cGenColor","f08080")
params["cL1Name"] = fs.formdata.getvalue("cL1Name","blue")
params["cL2Name"] = fs.formdata.getvalue("cL2Name","green")
params["cL3Name"] = fs.formdata.getvalue("cL3Name","black")
params["cL4Name"] = fs.formdata.getvalue("cL4Name","pink")
params["cL5Name"] = fs.formdata.getvalue("cL5Name","orange")
params["cL6Name"] = fs.formdata.getvalue("cL6Name","red")
params["cL1Color"] = fs.formdata.getvalue("cL1Color","0000ff")
params["cL2Color"] = fs.formdata.getvalue("cL2Color","00ff00")
params["cL3Color"] = fs.formdata.getvalue("cL3Color","000000")
params["cL4Color"] = fs.formdata.getvalue("cL4Color","ffc0cb")
params["cL5Color"] = fs.formdata.getvalue("cL5Color","ffa500")
params["cL6Color"] = fs.formdata.getvalue("cL6Color","ff0000")
params["L1style"] = fs.formdata.getvalue("L1style","bold")
params["L2style"] = fs.formdata.getvalue("L2style","")
params["L3style"] = fs.formdata.getvalue("L3style","dashed")
params["L4style"] = fs.formdata.getvalue("L4style","dashed")
params["L5style"] = fs.formdata.getvalue("L5style","")
params["L6style"] = fs.formdata.getvalue("L6style","bold")
if params["splines"] == "yes":
params["splineName"] = "curves"
else:
params["splineName"] = "lines"
if params["nodeshape"] == "yes":
params["nodeshapeType"] = "box"
else:
params["nodeshapeType"] = "ellipse"
if params["whichValue"] == 0:
params["correlationName"] = "Pearson"
elif params["whichValue"] == 1:
params["correlationName"] = "Spearman"
elif params["whichValue"] == 2:
params["correlationName"] = "Literature"
else:
params["correlationName"] = "Tissue"
# see graphviz::writeNeatoFile to find out what this done
params["edges"] = "complex"
return params
def buildParamDict(cursor, fd):
params = {}
fs = fd.formdata #cgi.FieldStorage()
params["progress"] = fs.getfirst("progress", "0")
params["filename"] = fs.getfirst("filename", "")
if params["filename"] == "":
raise MultitraitException("Required parameter filename missing.")
params["targetDatabase"] = fs.getfirst("targetDatabase", "U74Av2RMA_Raw_ProbeSet_March04")
params["firstRun"] = webqtlUtil.safeInt(fs.getfirst("firstRun", "0"),0)
params["threshold"] = webqtlUtil.safeFloat(fs.getfirst("threshold", "0.5"), 0.5)
params["subsetSize"] = webqtlUtil.safeInt(fs.getfirst("subsetSize", "10"), 10)
if params["subsetSize"] < -1:
params["subsetSize"] = -1
params["correlation"] = fs.getfirst("correlation", "pearson")
params["subsetCount"] = webqtlUtil.safeInt(fs.getfirst("subsetCount", 10), 10)
if params["subsetCount"] < -1:
params["subsetCount"] = -1
#params["outputType"] = fs.getfirst("outputType", "html")
#if params["outputType"] not in ("html", "text"):
# params["outputType"] = "html"
if params["correlation"] not in ("pearson", "spearman"):
params["correlation"] = "pearson"
params["correlationName"] = params["correlation"].capitalize()
# one of two cases:
# 1) We have just come from a submit, so there are a bunch of display*
# but no displaySets. Thus, the code down there converts the display*
# to displaySets so the GET request doesn't get too long
# 2) We have just been redirected from a progress page which already has
# a converted displaySets for us.
displaySets = webqtlUtil.safeInt(fs.getfirst("displaySets","0"), 0)
if displaySets == 0:
for key in fs.keys():
if key[:7] == "display":
#print "Hit display key %s<br>" % key
try:
whichSet = int(key[7:])
# prevent malicious attacks
whichSet = min(whichSet, 512)
displaySets += pow(2, whichSet)
except ValueError: pass
params["displaySets"] = displaySets
#print "In the beginning, display sets was %s: %s<br>" % (displaySets,
# str(binaryDecompose(displaySets)))
# if we are just gonna display a progress page, then there's no
# reason to look up detailed database information
#if params["progress"] == "1":
# return params
a,b = trait.dbNameToTypeId(cursor, params["targetDatabase"]) # XZ, 09/10/2008: add module name
params["targetDatabaseType"] = a
params["targetDatabaseId"] = b
params["targetDatabaseName"] = params["targetDatabase"]
return params