Add all the source codes into the github.

1 files changed, 153 insertions, 0 deletions

diff --git a/web/webqtl/utility/AJAX_table.py b/web/webqtl/utility/AJAX_table.py
new file mode 100755
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+++ b/web/webqtl/utility/AJAX_table.py
@@ -0,0 +1,153 @@
+# 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)