Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 143 deletions

diff --git a/web/webqtl/externalResource/ODEPage.py b/web/webqtl/externalResource/ODEPage.py
deleted file mode 100755
index f02fe5aa..00000000
--- a/web/webqtl/externalResource/ODEPage.py
+++ /dev/null
@@ -1,143 +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
-
-#ODEPage.py
-
-import string
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from base.webqtlTrait import webqtlTrait
-from base.templatePage import templatePage
-from dbFunction import webqtlDatabaseFunction
-		
-class ODEPage(templatePage):
-
-    def __init__(self,fd):
-
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-            return
-
-        #XZ, self.theseTraits holds the "ProbeSet" traits.
-        self.theseTraits = []
-
-        self.searchResult = fd.formdata.getvalue('searchResult', [])
-        if type("1") == type(self.searchResult):
-            self.searchResult = [self.searchResult]
-
-        for item in self.searchResult:
-            try:
-                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-                thisTrait.retrieveInfo(QTL=1)
-                if thisTrait.db.type == "ProbeSet":
-                    self.theseTraits.append(thisTrait)
-            except:
-                pass
-
-        if self.theseTraits:
-            pass
-        else:
-            heading = 'ODE'
-            detail = ['You need to select at least one microarray trait to submit.']
-            self.error(heading=heading,detail=detail)
-            return
-
-        chipName = self.getChipName(fd)
-        species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
-
-        if species == 'rat':
-            species = 'Rattus norvegicus'
-        elif species == 'human':
-            species = 'Homo sapiens'
-        elif species == 'mouse':
-            species = 'Mus musculus'
-        else:
-            species = ''
-
-        probesetNameList = self.getProbesetNameList(fd)
-
-        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
-
-        formODE = HT.Form(cgi="http://ontologicaldiscovery.org/index.php?action=manage&cmd=importGeneSet", enctype='multipart/form-data', name='formODE', submit = HT.Input(type='hidden'))
-
-        hddnODE = {}
-
-        hddnODE['client'] = 'genenetwork'
-        hddnODE['species'] = species
-        hddnODE['idtype'] = chipName
-        hddnODE['list'] = string.join(probesetNameList, ",")
-
-        for key in hddnODE.keys():
-            formODE.append(HT.Input(name=key, value=hddnODE[key], type='hidden'))
-
-        TD_LR.append(formODE)
-
-        TD_LR.append(HT.Paragraph("Your selections of %d traits is being exported to the ODE" % len(self.theseTraits), Class="cr fs16 fwb", align="Center"))
-        # updated by NL, moved mixedChipError() to webqtl.js and change it to mixedChipError(methodName)		
-        if chipName == 'mixed':
-            methodName = "ODE" 	
-            self.dict['js1'] = """
-                <SCRIPT LANGUAGE="JavaScript">
-                    setTimeout("mixedChipError('%s')",1000);
-                </SCRIPT>
-                        """ % methodName 
-        else:
-            self.dict['js1'] = """
-                <SCRIPT LANGUAGE="JavaScript">
-                    setTimeout('document.formODE.submit()',1000);
-                </SCRIPT>
-                """
-
-        self.dict['body'] = TD_LR
-
-
-
-    def getProbesetNameList(self, fd):
-        probesetNameList = []
-
-        for item in self.theseTraits:
-            probesetNameList.append(item.name)
-
-        return probesetNameList
-
-
-
-    def getChipName(self, fd):
-        chipName0 = ""
-        for item in self.theseTraits:
-            self.cursor.execute('SELECT GeneChip.Name FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % item.db.name)
-            chipName = self.cursor.fetchone()[0]
-            if chipName != chipName0:
-                if chipName0:
-                    return 'mixed'
-                else:
-                    chipName0 = chipName
-            else:
-                pass
-
-        return chipName