Add all the source codes into the github.

1 files changed, 143 insertions, 0 deletions

diff --git a/web/webqtl/externalResource/ODEPage.py b/web/webqtl/externalResource/ODEPage.py
new file mode 100755
index 00000000..f02fe5aa
--- /dev/null
+++ b/web/webqtl/externalResource/ODEPage.py
@@ -0,0 +1,143 @@
+# 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