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Diffstat (limited to 'web/webqtl/compareCorrelates/htmlModule.py')
| -rwxr-xr-x | web/webqtl/compareCorrelates/htmlModule.py | 279 |
1 files changed, 0 insertions, 279 deletions
diff --git a/web/webqtl/compareCorrelates/htmlModule.py b/web/webqtl/compareCorrelates/htmlModule.py deleted file mode 100755 index ebba3b86..00000000 --- a/web/webqtl/compareCorrelates/htmlModule.py +++ /dev/null @@ -1,279 +0,0 @@ -# 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 - |