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Diffstat (limited to 'wqflask/utility/AJAX_table.py')
| -rwxr-xr-x | wqflask/utility/AJAX_table.py | 153 |
1 files changed, 153 insertions, 0 deletions
diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py new file mode 100755 index 00000000..963a530e --- /dev/null +++ b/wqflask/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) |