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+# 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