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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/utility/AJAX_table.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
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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 cPickle
+import os
+import MySQLdb
+import time
+import pyXLWriter as xl
+
+from htmlgen import HTMLgen2 as HT
+
+from base import webqtlConfig
+from THCell import THCell
+from TDCell import TDCell
+import webqtlUtil
+
+
+class AJAX_table:
+ def __init__(self, fd):
+ file = fd.formdata.getfirst("file", "")
+ sort = fd.formdata.getfirst("sort", "")
+ order = fd.formdata.getfirst("order", "up")
+ cmd = fd.formdata.getfirst("cmd", "")
+ tableID = fd.formdata.getfirst("tableID", "")
+ addIndex = fd.formdata.getfirst("addIndex", "1")
+ hiddenColumnsString = fd.formdata.getfirst("hiddenColumns", "")
+ hiddenColumns = hiddenColumnsString.split(',')
+
+ try:
+ fp = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'rb')
+ tblobj = cPickle.load(fp)
+ fp.close()
+
+ if cmd == 'addCorr':
+ dbId = int(fd.formdata.getfirst("db"))
+ dbFullName = fd.formdata.getfirst("dbname")
+ trait = fd.formdata.getfirst("trait")
+ form = fd.formdata.getfirst("form")
+ ids = fd.formdata.getfirst("ids")
+ vals = fd.formdata.getfirst("vals")
+ ids = eval(ids)
+ nnCorr = len(ids)
+ vals = eval(vals)
+
+ workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file))
+ worksheet = workbook.add_worksheet()
+
+ con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
+ cursor = con.cursor()
+
+ cursor.execute("Select name, ShortName from ProbeSetFreeze where Id = %s", dbId)
+ dbName, dbShortName = cursor.fetchone()
+
+ tblobj['header'][0].append(
+ THCell(HT.TD(dbShortName, Class="fs11 ffl b1 cw cbrb"),
+ text="%s" % dbShortName, idx=tblobj['header'][0][-1].idx + 1),
+ )
+
+ headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")
+ for i, item in enumerate(tblobj['header'][0]):
+ if (i > 0):
+ worksheet.write([8, i-1], item.text, headingStyle)
+ worksheet.set_column([i-1, i-1], 2*len(item.text))
+
+ for i, row in enumerate(tblobj['body']):
+ ProbeSetId = row[1].text
+ #XZ, 03/02/2009: Xiaodong changed Data to ProbeSetData
+ cursor.execute("""
+ Select ProbeSetData.StrainId, ProbeSetData.Value
+ From ProbeSetData, ProbeSetXRef, ProbeSet
+ where ProbeSetXRef.ProbeSetFreezeId = %d AND
+ ProbeSetXRef.DataId = ProbeSetData.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSet.Name = '%s'
+ """ % (dbId, ProbeSetId))
+ results = cursor.fetchall()
+ vdict = {}
+ for item in results:
+ vdict[item[0]] = item[1]
+ newvals = []
+ for id in ids:
+ if vdict.has_key(id):
+ newvals.append(vdict[id])
+ else:
+ newvals.append(None)
+ corr,nOverlap= webqtlUtil.calCorrelation(newvals,vals,nnCorr)
+ repr = '%0.4f' % corr
+ row.append(
+ TDCell(HT.TD(HT.Href(text=repr, url="javascript:showCorrPlotThird('%s', '%s', '%s')" % (form, dbName, ProbeSetId), Class="fs11 fwn ffl"), " / ", nOverlap, Class="fs11 fwn ffl b1 c222", align="middle"),repr,abs(corr))
+ )
+
+ last_row=0
+ for j, item in enumerate(tblobj['body'][i]):
+ if (j > 0):
+ worksheet.write([9+i, j-1], item.text)
+ last_row = 9+i
+ last_row += 1
+
+ titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
+ ##Write title Info
+ # Modified by Hongqiang Li
+ worksheet.write([0, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
+ worksheet.write([1, 0], "Trait : %s" % trait, titleStyle)
+ worksheet.write([2, 0], "Database : %s" % dbFullName, titleStyle)
+ worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
+ worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
+ worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
+ #Write footer info
+ worksheet.write([1 + last_row, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
+ worksheet.write([2 + last_row, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
+
+ cursor.close()
+ workbook.close()
+
+ objfile = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'wb')
+ cPickle.dump(tblobj, objfile)
+ objfile.close()
+ else:
+ pass
+
+ self.value = str(webqtlUtil.genTableObj(tblobj=tblobj, file=file, sortby=(sort, order), tableID = tableID, addIndex = addIndex, hiddenColumns = hiddenColumns))
+
+ except:
+ self.value = "<span class='fs16 fwb cr ffl'>The table is no longer available on this server</span>"
+
+ def __str__(self):
+ return self.value
+
+ def write(self):
+ return str(self)