aboutsummaryrefslogtreecommitdiff
path: root/wqflask/utility/AJAX_table.py
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/utility/AJAX_table.py')
-rw-r--r--wqflask/utility/AJAX_table.py155
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)