Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into production

1 files changed, 0 insertions, 155 deletions

diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py
deleted file mode 100644
index d70acfcd..00000000
--- a/wqflask/utility/AJAX_table.py
+++ /dev/null
@@ -1,155 +0,0 @@
-# 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()
-
-                logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
-
-                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)