# 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)