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