# 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 sys import string import os import MySQLdb import cgi from htmlgen import HTMLgen2 as HT from base import webqtlConfig # XZ 08/14/2008: When I tried to replace 'from webqtlConfig import *' with 'import webqtlConfig' # XZ 08/14/2008: I found some problems. I discussed with Hongqiang and the below is conclusion. # XZ 08/14/2008: The program uses webqtlConfig.DB_NAME, webqtlConfig.MYSQL_SERVER and so on # XZ 08/14/2008: without 'import webqtlConfig'. This program will not work. # XZ 08/14/2008: CONFIG_htmlpath doesn't exist in webqtlConfig.py # XZ 08/14/2008: Hongqian said this was done by Fan Zhang, and this program was not tested. # XZ 08/14/2008: So nobody realize these bugs. # XZ, 09/09/2008: This function is not called any where. # XZ, 09/09/2008: Actually, I don't think this function works. def genHeaderFooter(i=1,title='',basehref='',js1='',js2='',layer='',body=''): """ generate footer and header HTML code default is header i = 0 is footer+header i = 1 is header i = 2 is footer """ try: temp_file = CONFIG_htmlpath + 'beta-template.html' fp = open(temp_file, 'rb') template = fp.read() fp.close() template = template % (title,basehref,js1,js2,layer,body, "") header,footer = string.split(template,'<!-- split from Here -->') if i == 0: return header + footer elif i == 1: return header elif i == 2: return footer else: return "" except: if i == 0: return "header + footer" elif i == 1: return "header" elif i == 2: return "footer" else: return "" # XZ, 09/09/2008: This function is only used in multitrait.py where it is called with value assigned to db. # XZ, 09/09/2008: So the try-except block is not executed. # XZ, 09/09/2008: This explains why no error was generated even without 'import webqtlConfig' def genDatabaseMenu(db = None, public =1, RISetgp = 'BXD', selectname = 'database', selected = ""): """ generate database Menu public = 0 : search3.html databases Menu public = 1 : search.html databases Menu """ if not db: try: # import MySQLdb # con = MySQLdb.Connect(db='db_webqtl') # Modified by Fan Zhang con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) db = con.cursor() except: return "Connect MySQL Server Error" else: pass databaseMenu = HT.Select(name=selectname) nmenu = 0 # here's a hack: bxd and bxd300 can be correlated against each other # if either of those are the group, we put in special SQL that pulls both if RISetgp in ("BXD", "BXD300"): ibsNameQry = '(InbredSet.Name = "BXD" OR InbredSet.Name = "BXD300")' else: ibsNameQry = 'InbredSet.Name = "%s"' % RISetgp #Publish Database db.execute(''' SelecT PublishFreeze.FullName, PublishFreeze.Name from PublishFreeze, InbredSet where PublishFreeze.InbredSetId = InbredSet.Id and %s ''' % ibsNameQry) for item in db.fetchall(): databaseMenu.append(item) nmenu += 1 #Genome Database db.execute(''' SelecT GenoFreeze.FullName, GenoFreeze.Name from GenoFreeze,InbredSet where GenoFreeze.InbredSetId = InbredSet.Id and %s ''' % ibsNameQry) for item in db.fetchall(): databaseMenu.append(item) nmenu += 1 #Microarray Database db.execute('SelecT Id, Name from Tissue') for item in db.fetchall(): TId, TName = item databaseMenuSub = HT.Optgroup(label = '%s ------' % TName) db.execute(''' SelecT ProbeSetFreeze.FullName, ProbeSetFreeze.Name from ProbeSetFreeze, ProbeFreeze, InbredSet where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %d and ProbeSetFreeze.public > %d and ProbeFreeze.InbredSetId = InbredSet.Id and %s order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ''' % (TId,public,ibsNameQry)) for item2 in db.fetchall(): databaseMenuSub.append(item2) nmenu += 1 databaseMenu.append(databaseMenuSub) if nmenu: if selected: databaseMenu.selected.append(selected) return str(databaseMenu) else: return '' # XZ, 09/09/2008: This function is not called any where. # XZ, 09/09/2008: Actually, I don't think this function works. # XZ, 09/09/2008: There is no 'DataForm' file now. It should be webqtlForm.py def genRISample(): import glob import reaper import random import math import webqtlUtil risets = filter(lambda X:X.find('F2')<0, map(os.path.basename, glob.glob(os.path.join(CONFIG_genodir, "*.geno")))) risets = map(lambda X:X.split('.')[0], risets) risets.remove("BayXSha") risets.sort() body = HT.Blockquote() NPerRow = 6 for item in risets: values = [] if item == 'AXBXA': item2='AXB/BXA' elif item == 'HXBBXH': item2='HXB/BXH' else: item2=item body.append(HT.Paragraph(item2, Class='subtitle')) tbl = HT.TableLite(Class="collap") dataset = reaper.Dataset() dataset.read(os.path.join(CONFIG_genodir, "%s.geno"%item)) prgy = webqtlUtil.ParInfo[item] + list(dataset.prgy) mean = random.random()*100 variance = random.random()*500 variables = [] while len(variables) < len(prgy): S = 2 while (S>=1): U1= random.random() U2= random.random() V1= 2*U1-1.0 V2= 2*U2-1.0 S=V1*V1+V2*V2 X= math.sqrt(-2 * math.log(S) / S) * V1 Y= math.sqrt(-2 * math.log(S) / S) * V2 variables.append(mean + math.sqrt(variance) * X) variables.append(mean + math.sqrt(variance) * Y) tempTR = HT.TR() for i, strain in enumerate(prgy): if i and i%NPerRow==0: tbl.append(tempTR) tempTR = HT.TR() if random.random() < 0.2: variable = 'X' else: variable = "%2.3f" % variables[i] tempTR.append(HT.TD(strain, Class="strains", width=80)) tempTR.append(HT.TD(variable, Class="values", width=60)) values.append(variable) for j in range(NPerRow-i%NPerRow-1): tempTR.append(HT.TD()) tbl.append(tempTR) body.append(tbl) body.append(HT.Paragraph("Copy the following line to paste into the GeneNetwork entry box:")) body.append(HT.Code(string.join(values, " "))) body.append(HT.HR(width="90%")) return body if __name__ == "__main__": if os.environ.has_key('SCRIPT_FILENAME'): script_filename = os.environ['SCRIPT_FILENAME'] else: script_filename = '' #Used as cgi script if script_filename and script_filename[-2:] == 'py': print 'Content-type: text/html\n' formdata = cgi.FieldStorage() sys.stderr = sys.stdout try: getID = string.lower(formdata.getvalue('get')) except: getID = '' #Used as command else: if len(sys.argv) >= 2: getID = string.lower(sys.argv[1]) else: getID = '' if getID == 'headerfooter': print genHeaderFooter(0) elif getID == 'header': print genHeaderFooter(1) elif getID == 'footer': print genHeaderFooter(2) elif getID == 'databasemenu': print genDatabaseMenu(public=0) elif getID == 'datasample': print genRISample() else: print genHeaderFooter(0) else: pass