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-rwxr-xr-xweb/webqtl/externalResource/ODEPage.py143
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