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

1 files changed, 0 insertions, 699 deletions

diff --git a/web/webqtl/main.py b/web/webqtl/main.py
deleted file mode 100644
index f37fae01..00000000
--- a/web/webqtl/main.py
+++ /dev/null
@@ -1,699 +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
-
-
-from mod_python import apache, util, Session, Cookie
-import time
-import string
-
-from base.webqtlFormData import webqtlFormData
-
-import logging
-logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
-_log = logging.getLogger("main")
-
-
-
-def handler(req):
-	_log.info("Handling a request")
-	req.content_type = 'text/html'
-
-	formdata = util.FieldStorage(req)
-
-	formID = formdata.getfirst('FormID')
-	sid = formdata.getfirst('sid')
-	cmdID = formdata.getfirst('cmd')
-	page = None
-
-	#XZ: this statement must be put into handler function
-	_log.info("Loading session")
-	mod_python_session = Session.Session(req, timeout=864000, lock=0)
-	mod_python_session.load()			
-	_log.info("Done loading session")
-
-	if sid:
-		from cmdLine import procPage
-		reload(procPage)
-		req.content_type = 'text/html'
-		procPage.procPage(sid, req)
-	else:	
-		fd = webqtlFormData(req=req, mod_python_session=mod_python_session, FieldStorage_formdata=formdata)
-
-		if formID:
-		        _log.info("Dispatching on %s, %s"%(formID, fd.formID))
-			#XZ: Special case. Pay attention to parameters! We can NOT pass 'fd'!
-                        if fd.formID == 'uploadFile':
-				from base import cookieData
-				from misc import uploadFilePage
-				reload(uploadFilePage)
-				reload(cookieData)
-				cookies = cookieData.cookieData(Cookie.get_cookies(req)) #new module
-				req.content_type = 'text/html'
-				page = uploadFilePage.uploadFilePage(fd, formdata, cookies)
-
-                        #search
-                        elif fd.formID in ('searchResult','asearchResult'):
-                                from search import SearchResultPage
-                                reload(SearchResultPage)
-                                req.content_type = 'text/html'
-                                page = SearchResultPage.SearchResultPage(fd)
-
-                        #showTrait
-                        elif fd.formID == 'showDatabase':
-                                from showTrait import ShowTraitPage
-                                reload(ShowTraitPage)
-                                req.content_type = 'text/html'
-                                page = ShowTraitPage.ShowTraitPage(fd)
-                        elif fd.formID == 'showBest':
-                                from showTrait import ShowBestTrait
-                                reload(ShowBestTrait)
-                                req.content_type = 'text/html'
-                                page = ShowBestTrait.ShowBestTrait(fd)
-                        elif fd.formID == 'showProbeInfo':
-                                from showTrait import ShowProbeInfoPage
-                                reload(ShowProbeInfoPage)
-                                page = ShowProbeInfoPage.ShowProbeInfoPage(fd)
-                                req.content_type = 'text/html'
-			elif fd.formID in ('crossChoice', 'varianceChoice'):
-				if not fd.submitID:
-					req.content_type = 'text/html'
-					req.write('check your page')
-				elif fd.submitID == 'sample':
-					from showTrait import testTraitPage  # new module
-					reload(testTraitPage)
-					page = testTraitPage.testTraitPage()
-					req.content_type = 'text/html'
-				else:
-					from showTrait import DataEditingPage
-					reload(DataEditingPage)
-					req.content_type = 'text/html'
-					page = DataEditingPage.DataEditingPage(fd)
-
-			#from Trait Data and Analysis form page
-			elif fd.formID == 'dataEditing':
-				if not fd.submitID:
-					req.content_type = 'text/html'
-					req.write('check your page')
-				elif fd.submitID == 'basicStatistics': #Updated Basic Statistics page (pop-up when user hits "update" button in DataEditingPage.py
-					from basicStatistics import updatedBasicStatisticsPage
-                                        reload(updatedBasicStatisticsPage)
-                                        req.content_type = 'text/html'
-                                        page = updatedBasicStatisticsPage.updatedBasicStatisticsPage(fd)
-                                elif fd.submitID == 'updateRecord':
-                                        from updateTrait import DataUpdatePage
-                                        reload(DataUpdatePage)
-                                        req.content_type = 'text/html'
-                                        page=DataUpdatePage.DataUpdatePage(fd)
-                                elif fd.submitID == 'addRecord':
-                                        from collection import AddUserInputToSelectionPage
-                                        reload(AddUserInputToSelectionPage)
-                                        page = AddUserInputToSelectionPage.AddUserInputToSelectionPage(fd)
-                                        req.content_type = 'text/html'
-                                elif fd.submitID == 'addPublish':
-                                        from submitTrait import AddUserInputToPublishPage
-                                        reload(AddUserInputToPublishPage)
-                                        req.content_type = 'text/html'
-                                        page = AddUserInputToPublishPage.AddUserInputToPublishPage(fd)
-                                elif fd.submitID == 'correlation':
-                                        from cmdLine import cmdCorrelationPage
-                                        reload(cmdCorrelationPage)
-                                        page = cmdCorrelationPage.cmdCorrelationPage(fd)
-                                elif fd.submitID == 'intervalMap':
-                                        from cmdLine import cmdIntervalMappingPage
-                                        reload(cmdIntervalMappingPage)
-                                        page = cmdIntervalMappingPage.cmdIntervalMappingPage(fd)
-				elif fd.submitID == 'markerRegression':
-					from cmdLine import cmdMarkerRegressionPage
-					reload(cmdMarkerRegressionPage)
-					req.content_type = 'text/html'
-					page = cmdMarkerRegressionPage.cmdMarkerRegressionPage(fd)
-
-				elif fd.submitID == 'directPlot':
-					from cmdLine import cmdDirectPlotPage
-					reload(cmdDirectPlotPage)
-					req.content_type = 'text/html'
-					page = cmdDirectPlotPage.cmdDirectPlotPage(fd)
-				elif fd.submitID == 'exportData':
-					from showTrait import exportPage
-					reload(exportPage)
-					req.content_type = 'text/html'
-					page = exportPage.ExportPage(fd)
-				elif fd.submitID == 'showAll':
-					from cmdLine import cmdShowAllPage
-					reload(cmdShowAllPage)
-					page = cmdShowAllPage.cmdShowAllPage(fd)
-				elif fd.submitID == 'showAll2':
-					from cmdLine import cmdShowAllPage2
-					reload(cmdShowAllPage2)
-					page=cmdShowAllPage2.cmdShowAllPage2(fd)
-				else:
-					pass
-
-			#from marker regression result page
-                        elif fd.formID == 'secondRegression':
-                                if not fd.submitID:
-                                        req.content_type = 'text/html'
-                                        req.write('check your page')
-                                elif fd.submitID == 'compositeRegression':
-                                        req.content_type = 'text/html'
-                                        from markerRegression import CompositeMarkerRegressionPage
-                                        reload(CompositeMarkerRegressionPage)
-                                        page = CompositeMarkerRegressionPage.CompositeMarkerRegressionPage(fd)
-                                elif fd.submitID == 'intervalMap':
-                                        from intervalMapping import IntervalMappingPage
-                                        reload(IntervalMappingPage)
-                                        page = IntervalMappingPage.IntervalMappingPage(fd)
-                                else:
-                                        pass
-
-			#cmdLine	
-			elif fd.formID == 'showIntMap':
-				from cmdLine import cmdIntervalMappingPage
-				reload(cmdIntervalMappingPage)
-				page = cmdIntervalMappingPage.cmdIntervalMappingPage(fd)
-                        elif fd.formID == 'heatmap':
-                                from cmdLine import cmdHeatmapPage
-                                reload(cmdHeatmapPage)
-                                page = cmdHeatmapPage.cmdHeatmapPage(fd)
-                        elif fd.formID == 'networkGraph':
-                                from cmdLine import cmdNetworkGraphPage
-                                reload(cmdNetworkGraphPage)
-                                page = cmdNetworkGraphPage.cmdNetworkGraphPage(fd)
-                        elif fd.formID == 'compCorr2':
-                                from cmdLine import cmdCompCorrPage
-                                reload(cmdCompCorrPage)
-                                page = cmdCompCorrPage.cmdCompCorrPage(fd)
-                        elif fd.formID == 'calPartialCorrDB':
-                                from cmdLine import cmdPartialCorrelationPage
-                                reload(cmdPartialCorrelationPage)
-                                page = cmdPartialCorrelationPage.cmdPartialCorrelationPage(fd)
-				
-			#pairScan
-			elif fd.formID == 'showCategoryGraph':
-				from pairScan import CategoryGraphPage
-				reload(CategoryGraphPage)
-				req.content_type = 'text/html'
-				page = CategoryGraphPage.CategoryGraphPage(fd)
-			elif fd.formID == 'pairPlot':
-				from pairScan import PairPlotPage
-				reload(PairPlotPage)
-				req.content_type = 'text/html'
-				page = PairPlotPage.PairPlotPage(fd)
-
-			#compareCorrelates
-			elif fd.formID == 'compCorr':
-				from compareCorrelates import MultipleCorrelationPage
-				reload(MultipleCorrelationPage)
-				page = MultipleCorrelationPage.MultipleCorrelationPage(fd)
-
-			#correlationMatrix
-			elif fd.formID == 'corMatrix':
-				from correlationMatrix import CorrelationMatrixPage
-				reload(CorrelationMatrixPage)
-				req.content_type = 'text/html'
-				page = CorrelationMatrixPage.CorrelationMatrixPage(fd)
-                        elif fd.formID=='tissueCorrelation' or fd.formID=='dispMultiSymbolsResult':
-                                from correlationMatrix import TissueCorrelationPage
-                                reload(TissueCorrelationPage)
-                                page = TissueCorrelationPage.TissueCorrelationPage(fd)
-			elif fd.formID =='dispTissueCorrelationResult':
-				from cmdLine import cmdTissueCorrelationResultPage
-				reload (cmdTissueCorrelationResultPage)
-				page = cmdTissueCorrelationResultPage.cmdTissueCorrelationResultPage(fd)
-			elif fd.formID=='tissueAbbreviation':
-				from correlationMatrix import TissueAbbreviationPage
-				reload(TissueAbbreviationPage)
-				page = TissueAbbreviationPage.TissueAbbreviationPage(fd)
-			
-			#collection
-			elif fd.formID == 'dispSelection':
-				from collection import DisplaySelectionPage
-				reload(DisplaySelectionPage)
-				page = DisplaySelectionPage.DisplaySelectionPage(fd)
-				req.content_type = 'text/html'
-			elif fd.formID == 'addToSelection':
-				from collection import AddToSelectionPage
-				reload(AddToSelectionPage)
-				page = AddToSelectionPage.AddToSelectionPage(fd)
-				req.content_type = 'text/html'
-			elif fd.formID == 'removeSelection':
-				from collection import RemoveSelectionPage
-				reload(RemoveSelectionPage)
-				page = RemoveSelectionPage.RemoveSelectionPage(fd)
-				req.content_type = 'text/html'
-			elif fd.formID == 'exportSelect':
-				from collection import ExportSelectionPage
-				reload(ExportSelectionPage)
-				page = ExportSelectionPage.ExportSelectionPage(fd)
-			elif fd.formID == 'importSelect':
-				from collection import ImportSelectionPage
-				reload(ImportSelectionPage)
-				page = ImportSelectionPage.ImportSelectionPage(fd)
-				req.content_type = 'text/html'
-			elif fd.formID == 'exportSelectionDetailInfo':
-				from collection import ExportSelectionDetailInfoPage
-				reload(ExportSelectionDetailInfoPage)
-				page = ExportSelectionDetailInfoPage.ExportSelectionDetailInfoPage(fd)
-                        elif fd.formID == 'batSubmitResult':
-                                from collection import BatchSubmitSelectionPage
-                                reload(BatchSubmitSelectionPage)
-                                page = BatchSubmitSelectionPage.BatchSubmitSelectionPage(fd)
-                                req.content_type = 'text/html'
-
-			#user
-			elif fd.formID == 'userLogin':
-				from user import userLogin
-				reload(userLogin)
-				page = userLogin.userLogin(fd)
-				req.content_type = 'text/html'
-			elif fd.formID == 'userLogoff':
-				from user import userLogoff
-				reload(userLogoff)
-				page = userLogoff.userLogoff(fd)
-				req.content_type = 'text/html'
-			elif fd.formID == 'userPasswd':
-				from user import userPasswd
-				reload(userPasswd)
-				page = userPasswd.userPasswd(fd)
-				req.content_type = 'text/html'
-
-			#submitTrait
-                        elif fd.formID == 'pre_dataEditing':
-                                from submitTrait import VarianceChoicePage
-                                reload(VarianceChoicePage)
-                                page = VarianceChoicePage.VarianceChoicePage(fd)
-                                req.content_type = 'text/html'
-			elif fd.formID == 'batSubmit':
-				from submitTrait import BatchSubmitPage
-				reload(BatchSubmitPage)
-				req.content_type = 'text/html'
-				page = BatchSubmitPage.BatchSubmitPage(fd)
-
-
-			#misc
-                        elif fd.formID == 'editHtml':
-                                from misc import editHtmlPage
-                                reload(editHtmlPage)
-                                req.content_type = 'text/html'
-                                page = editHtmlPage.editHtmlPage(fd)
-
-			#genomeGraph
-			elif fd.formID == 'transciptMapping':
-				from genomeGraph import cmdGenomeScanPage
-				reload(cmdGenomeScanPage)
-				req.content_type = 'text/html'
-				page = cmdGenomeScanPage.cmdGenomeScanPage(fd)
-			elif fd.formID == 'genAllDbResult':
-				from genomeGraph import genAllDbResultPage
-				reload(genAllDbResultPage)
-				page = genAllDbResultPage.genAllDbResultPage(fd)	
-
-			#geneWiki
-			elif fd.formID == 'geneWiki':
-				from geneWiki import AddGeneRIFPage
-				reload(AddGeneRIFPage)
-				page = AddGeneRIFPage.AddGeneRIFPage(fd)
-
-			#externalResource
-			elif fd.formID == 'GOTree':
-				from externalResource import GoTreePage
-				reload(GoTreePage)
-				req.content_type = 'text/html'
-				page = GoTreePage.GoTreePage(fd)
-			elif fd.formID == 'ODE':
-                                from externalResource import ODEPage
-                                reload(ODEPage)
-                                req.content_type = 'text/html'
-                                page = ODEPage.ODEPage(fd)
-                        elif fd.formID == 'GCAT':
-                                from externalResource import GCATPage
-                                reload(GCATPage)
-                                req.content_type = 'text/html'
-                                page = GCATPage.GCATPage(fd)
-
-			#management
-                        elif fd.formID == 'managerMain':
-                                from management import managerMainPage
-                                reload(managerMainPage)
-                                req.content_type = 'text/html'
-                                page = managerMainPage.managerMainPage(fd)
-                        elif fd.formID == 'createUserAccount':
-                                from management import createUserAccountPage
-                                reload(createUserAccountPage)
-                                req.content_type = 'text/html'
-                                page = createUserAccountPage.createUserAccountPage(fd)
-                        elif fd.formID == 'assignUserToDataset':
-                                from management import assignUserToDatasetPage
-                                reload(assignUserToDatasetPage)
-                                req.content_type = 'text/html'
-                                page = assignUserToDatasetPage.assignUserToDatasetPage(fd)
-                        elif fd.formID == 'deletePhenotypeTrait':
-                                from management import deletePhenotypeTraitPage
-                                reload(deletePhenotypeTraitPage)
-                                req.content_type = 'text/html'
-                                page = deletePhenotypeTraitPage.deletePhenotypeTraitPage(fd)	
-                        elif fd.formID == 'exportPhenotypeDataset':
-                                from management import exportPhenotypeDatasetPage
-                                reload(exportPhenotypeDatasetPage)
-                                req.content_type = 'text/html'
-                                page = exportPhenotypeDatasetPage.exportPhenotypeDatasetPage(fd)
-                        elif fd.formID == 'editHeaderFooter':
-                                from management import editHeaderFooter
-                                reload(editHeaderFooter)
-                                req.content_type = 'text/html'
-                                page = editHeaderFooter.editHeaderFooter(fd)
-			elif fd.formID == 'updGeno':
-                                from management import GenoUpdate
-                                reload(GenoUpdate)
-                                req.content_type = 'text/html'
-                                page = GenoUpdate.GenoUpdate(fd)
-
-			#correlation
-                        elif fd.formID == 'showCorrelationPlot':
-                                from correlation import PlotCorrelationPage
-                                reload(PlotCorrelationPage)
-                                req.content_type = 'text/html'
-                                page = PlotCorrelationPage.PlotCorrelationPage(fd)
-                        elif fd.formID == 'partialCorrInput':
-                                from correlation import PartialCorrInputPage
-                                reload(PartialCorrInputPage)
-                                req.content_type = 'text/html'
-                                page = PartialCorrInputPage.PartialCorrInputPage(fd)
-                        elif fd.formID == 'calPartialCorrTrait':
-                                from correlation import PartialCorrTraitPage
-                                reload(PartialCorrTraitPage)
-                                req.content_type = 'text/html'
-                                page = PartialCorrTraitPage.PartialCorrTraitPage(fd)
-
-			#elif fd.formID == 'BNInput':
-			#	from BN import BNInputPage
-			#	reload(BNInputPage)
-			#	req.content_type = 'text/html'
-			#	page = BNInputPage.BNInputPage(fd)
-
-                        elif fd.formID == 'updateRecord':
-				from updateTrait import DataUpdatePage
-				reload(DataUpdatePage)
-				req.content_type = 'text/html'
-				page=DataUpdatePage.DataUpdatePage(fd)
-
-			#schema
-			elif fd.formID == 'schemaShowPage':
-				from schema import ShowSchemaPage
-				reload(ShowSchemaPage)
-				req.content_type = 'text/html'
-				page = ShowSchemaPage.ShowSchemaPage(fd)
-			elif fd.formID == 'schemaShowComment':
-				from schema import ShowCommentPage
-				reload(ShowCommentPage)
-				req.content_type = 'text/html'
-				page = ShowCommentPage.ShowCommentPage(fd)
-			elif fd.formID == 'schemaUpdateComment':
-				from schema import UpdateCommentPage
-				reload(UpdateCommentPage)
-				req.content_type = 'text/html'
-				page = UpdateCommentPage.UpdateCommentPage(fd)
-
-			#snpBrowser
-			elif fd.formID == 'snpBrowser':
-				req.content_type = 'text/html'
-				snpId = fd.formdata.getfirst('snpId')
-				if snpId:
-					from snpBrowser import snpDetails
-					reload(snpDetails)
-					page = snpDetails.snpDetails(fd, snpId)
-				else:
-					from snpBrowser import snpBrowserPage
-					reload(snpBrowserPage)
-					page = snpBrowserPage.snpBrowserPage(fd)
-			elif fd.formID =='SnpBrowserResultPage':
-				from cmdLine import cmdSnpBrowserResultPage
-				reload (cmdSnpBrowserResultPage)
-				page = cmdSnpBrowserResultPage.cmdSnpBrowserResultPage(fd)
-
-			#intervalAnalyst
-			elif fd.formID == 'intervalAnalyst':
-				from intervalAnalyst import IntervalAnalystPage
-				reload(IntervalAnalystPage)
-				req.content_type = 'text/html'
-				page = IntervalAnalystPage.IntervalAnalystPage(fd)			
-
-			#AJAX_table
-			elif fd.formID == 'AJAX_table':
-				from utility import AJAX_table
-				reload(AJAX_table)
-				req.content_type = 'text/html'
-				req.write(AJAX_table.AJAX_table(fd).write())
-
-                      	elif fd.formID == 'submitSingleTrait':
-				from submitTrait import CrossChoicePage
-				reload(CrossChoicePage)
-				page = CrossChoicePage.CrossChoicePage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'sharing':
-				from dataSharing import SharingPage
-				reload(SharingPage)
-				page = SharingPage.SharingPage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'sharinginfo':
-				from dataSharing import SharingInfoPage
-				reload(SharingInfoPage)
-				page = SharingInfoPage.SharingInfoPage(fd)
-				req.content_type = 'text/html'
-			
-			elif fd.formID == 'sharinginfoedit':
-				from dataSharing import SharingInfoEditPage
-				reload(SharingInfoEditPage)
-				page = SharingInfoEditPage.SharingInfoEditPage(fd)
-				req.content_type = 'text/html'
-				
-			elif fd.formID == 'sharinginfodelete':
-				from dataSharing import SharingInfoDeletePage
-				reload(SharingInfoDeletePage)
-				page = SharingInfoDeletePage.SharingInfoDeletePage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'sharinginfoupdate':
-				from dataSharing import SharingInfoUpdatePage
-				reload(SharingInfoUpdatePage)
-				page = SharingInfoUpdatePage.SharingInfoUpdatePage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'sharingListDataset':
-				from dataSharing import SharingListDataSetPage
-				reload(SharingListDataSetPage)
-				page = SharingListDataSetPage.SharingListDataSetPage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'sharinginfoadd':
-				from dataSharing import SharingInfoAddPage
-				reload(SharingInfoAddPage)
-				page = SharingInfoAddPage.SharingInfoAddPage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'annotation':
-				from annotation import AnnotationPage
-				reload(AnnotationPage)
-				page = AnnotationPage.AnnotationPage(fd)
-				req.content_type = 'text/html'
-
-			elif fd.formID == 'qtlminer':
-				from qtlminer import QTLminer
-                                reload(QTLminer)
-                                req.content_type = 'text/html'
-                                page = QTLminer.QTLminer(fd)
-			elif fd.formID == 'qtlminerresult':
-				from cmdLine import cmdQTLminerPage
-                                reload (cmdQTLminerPage)
-                                page = cmdQTLminerPage.cmdQTLminerPage(fd)
-
-			else:
-				from search import IndexPage
-				reload(IndexPage)
-				page = IndexPage.IndexPage(fd)
-				req.content_type = 'text/html'
-
-                        #elif fd.formID == 'updGeno':
-                        #       import GenoUpdate
-                        #       reload(GenoUpdate)
-                        #       req.content_type = 'text/html'
-                        #       page=GenoUpdate.GenoUpdate(fd)
-                        #elif fd.formID == 'updStrain':
-                        #       import StrainUpdate
-                        #       reload(StrainUpdate)
-                        #       req.content_type = 'text/html'
-                        #       page=StrainUpdate.StrainUpdate(fd)
-                        #elif fd.formID == 'showTextResult':
-                        #       import resultPage
-                        #       reload(resultPage)
-                        #       page = resultPage.ShowTextResult(fd)
-                        #elif fd.formID == 'showStrainInfo':
-                        #       import dataPage
-                        #       reload(dataPage)
-                        #       req.content_type = 'text/html'
-                        #       page = dataPage.ShowStrainInfoPage(fd)
-                        #elif fd.formID == 'showImage':
-                        #       import dataPage
-                        #       reload(dataPage)
-                        #       req.content_type = 'text/html'
-                        #       page = dataPage.ShowImagePage(fd)
-                        #XZ, 04/29/2009: There is one webpage gn/web/webqtl/blat.html and I have moved it to junk folder. This function is very old and I don't think it is being used.
-                        #elif fd.formID == 'BlatSearch':
-                        #       import miscPage
-                        #       reload(miscPage)
-                        #       page = miscPage.ShowBlatResult(fd)
-                        #elif fd.formID == 'admin':
-                        #       import adminPage
-                        #       reload(adminPage)
-                        #       req.content_type = 'text/html'
-                        #       page = adminPage.adminModifyPage(fd)
-
-		elif cmdID: 
-			#need to rewrite
-			cmdID = string.lower(cmdID)
-			if cmdID in ('get','trait','tra'):
-	                        from textUI import cmdGet
-				reload(cmdGet)
-				req.content_type = 'text/plain'
-				req.write(cmdGet.cmdGet(fd).write())
-			elif cmdID in ('help', 'hlp'):
-				from textUI import cmdHelp
-				reload(cmdHelp)
-				req.content_type = 'text/plain'
-				req.write(cmdHelp.cmdHelp(fd).write())
-			elif cmdID in ('correlation','cor','pea','pearson'):
-				from textUI import cmdCorrelation
-				reload(cmdCorrelation)	   
-				req.content_type = 'text/plain'
-				req.write(cmdCorrelation.cmdCorrelation(fd).write())
-			elif cmdID in ('map','marker'):
-				from textUI import cmdMap
-				reload(cmdMap)
-				req.content_type = 'text/plain'
-				req.write(cmdMap.cmdMap(fd).write())
-			elif cmdID in ('geno','gen','genotype'):
-				from textUI import cmdGeno
-				reload(cmdGeno)
-				req.content_type = 'text/plain'
-				req.write(cmdGeno.cmdGeno(fd).write())
-			elif cmdID in ('interval','int'):
-				from textUI import cmdInterval
-				reload(cmdInterval)
-				req.content_type = 'text/plain'
-				req.write(cmdInterval.cmdInterval(fd).write())
-			elif cmdID in ('show','shw'):
-				from textUI import cmdShowEditing
-				reload(cmdShowEditing)
-				req.content_type = 'text/html'
-				result = cmdShowEditing.cmdShowEditing(fd)
-				page = result.page
-			elif cmdID in ('search','sch'):
-				req.content_type = 'text/plain'
-				from textUI import cmdSearchGene
-				reload(cmdSearchGene)
-				result = cmdSearchGene.cmdSearchGene(fd)
-				page = result.page
-				req.write(result.text)
-
-			#elif cmdID in ('tst','Test'):
-			#	req.write('Content-type: application/x-download')
-			#	req.write('Content-disposition: attachment; filename=my.txt\n')
-			#	genotype_file = GENODIR + 'AKXD.geno'
-			#	fp = open(genotype_file)
-			#	line = fp.read()
-			#	fp.close()
-			#	req.write(line)
-			#XZ, 03/03/2009: This fuction must be initiated from URL
-			#XZ: http://www.genenetwork.org/webqtl/WebQTL.py?cmd=birn&species=mouse&tissue=Hippocampus&ProbeId=1436869_at&Strain=BXD1
-			#elif cmdID[0:4]=="birn":
-			#	req.content_type = 'text/plain'
-			#	import BIRN
-			#	reload(BIRN)
-			#	result = BIRN.birnSwitch(fd)
-			#	req.write(result.text)
-                        #elif cmdID in ('spear','spearman','spe'):
-                        #       import cmdSpearman  # new modules
-                        #       reload(cmdSpearman)
-                        #       req.content_type = 'text/plain'
-                        #       req.write(cmdSpearman.cmdSpearman(fd).write())
-                        #elif cmdID in ('snp','track'):
-                        #       import cmdSnpTrack  # new modules
-                        #       reload(cmdSnpTrack)
-                        #       req.content_type = 'text/plain'
-                        #       req.write(cmdSnpTrack.cmdSnpTrack(fd).write())
-
-			else:
-				req.content_type = 'text/html'
-				req.write("###Wrong Command")
-
-                ######## Create first page when called with no formID ########
-
-		else:
-			_log.info("Going to the search page")
-			from search import IndexPage
-                        reload(IndexPage)
-                        page = IndexPage.IndexPage(fd)
-                        req.content_type = 'text/html'
-	
-	if page:
-		#send Cookie first
-		if page.cookie:
-			for item in page.cookie:
-				if (item):
-					modcookie = Cookie.Cookie(item.name, item.value)
-					modcookie.path = item.path
-					if item.expire != None:
-						modcookie.expires = time.time() + item.expire
-					Cookie.add_cookie(req, modcookie)
-
-		#save session
-		if page.session_data_changed:
-			for one_key in page.session_data_changed.keys():
-				mod_python_session[one_key] = page.session_data_changed[one_key]
-			mod_python_session.save()
-
-
-		req.content_type= page.content_type
-
-		#send attachment
-		if page.redirection:
-			util.redirect(req, page.redirection)
-		elif page.content_disposition:
-			req.headers_out["Content-Disposition"] = page.content_disposition
-			req.write(page.attachment)
-		elif page.debug: # for debug
-			req.write(page.debug)
-		#send regular content
-		else:
-			req.write(page.write())
-	else:
-		pass
-		
-	return apache.OK
-	
-