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diff --git a/web/webqtl/compareCorrelates/htmlModule.py b/web/webqtl/compareCorrelates/htmlModule.py
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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 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
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 22:19:58 +0000