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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
import string
from base import webqtlConfig
from cmdClass import cmdClass
#########################################
# Get trait value Class
#########################################
class cmdGet(cmdClass):
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all">%s%s?cmd=%s&probeset=100001_at&db=bra03-03Mas5&probe=all</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
if not self.error:
self.readDB()
else:
self.contents.append(self.example)
self.contents.append(self.accessCode)
def readDB(self):
prefix, dbId = self.getDBId(self.database)
traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
try:
if not traitdata:
raise ValueError
traitdata = heads + list(traitdata)
if self.format == 'col':
self.formatCols(traitdata)
else:
self.formatRows(traitdata)
except:
self.contents.append('Error: no record was found')
self.contents.append(self.accessCode)
return
def formatCols(self, traitdata):
for item in traitdata:
lines = []
for item2 in item:
lines.append(item2)
lines = string.join(map(str,lines), '\t')
self.contents.append(lines)
def formatRows(self, traitdata):
for i in range(len(traitdata[0])):
lines = []
for j in range(len(traitdata)):
lines.append(traitdata[j][i])
lines = string.join(map(str,lines), '\t')
self.contents.append(lines)
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