Add all the source codes into the github.

1 files changed, 101 insertions, 0 deletions

diff --git a/web/webqtl/externalResource/GCATPage.py b/web/webqtl/externalResource/GCATPage.py
new file mode 100755
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+++ b/web/webqtl/externalResource/GCATPage.py
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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
+
+#GCATPage.py
+
+from htmlgen import HTMLgen2 as HT
+
+from base.webqtlTrait import webqtlTrait
+from base.templatePage import templatePage
+    
+
+#Implemented by Xiaodong
+class GCATPage(templatePage):
+
+    def __init__(self,fd):
+
+        self.theseTraits = []
+        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="middle")
+
+        templatePage.__init__(self, fd)
+
+        if not self.openMysql():
+            return
+
+        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:
+            templatePage.__init__(self, fd)
+            heading = 'GCAT'
+            detail = ['You need to select at least one microarray trait to submit to GCAT.']
+            self.error(heading=heading,detail=detail)
+            return
+
+        geneSymbolList = self.getGeneSymbolList()
+
+        geneSymbolSet = set(geneSymbolList)
+
+        if ( len(geneSymbolSet) < 500 ):
+            temp = '+'.join(geneSymbolSet)
+            GCATurl = "http://binf1.memphis.edu/gcat/?organism=mouse&subset=all&year=2010&geneInput=%s" % temp
+
+            self.dict['js1'] = """
+                <SCRIPT LANGUAGE="JavaScript">
+                setTimeout( 'window.location = "%s"', 2000 );
+                </SCRIPT>
+            """ % GCATurl
+
+            TD_LR.append(HT.Paragraph("Your selection of %d genes is being submitted to GCAT" % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
+        else:
+            TD_LR.append(HT.Paragraph("Your selection of %d genes exceeds the limit of 500. Please reduce your gene number to below the limit." % len(geneSymbolSet), Class="cr fs16 fwb", align="Center"))
+
+
+        self.dict['body'] = TD_LR
+
+
+    def getGeneSymbolList(self):
+        geneList = []
+
+        for item in self.theseTraits:
+            item.retrieveInfo()
+            geneList.append(str(item.symbol))
+		
+        return geneList
+
+