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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/main.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/main.py')
-rw-r--r--web/webqtl/main.py699
1 files changed, 699 insertions, 0 deletions
diff --git a/web/webqtl/main.py b/web/webqtl/main.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
+
+
+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
+
+