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

1 files changed, 0 insertions, 200 deletions

diff --git a/web/webqtl/collection/ExportSelectionDetailInfoPage.py b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
deleted file mode 100755
index 7238c797..00000000
--- a/web/webqtl/collection/ExportSelectionDetailInfoPage.py
+++ /dev/null
@@ -1,200 +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
-
-#ExportSelectionDetailInfoPage.py
-
-import string
-from htmlgen import HTMLgen2 as HT
-import os
-import time
-import pyXLWriter as xl
-
-import reaper
-
-from base import webqtlConfig
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base.webqtlTrait import webqtlTrait
-	
-		
-#########################################
-#      Export Selection DetailInfo Page
-#########################################
-class ExportSelectionDetailInfoPage(templatePage):
-
-	def __init__(self,fd):
-
-		templatePage.__init__(self, fd)
-		
-		if not self.openMysql():
-			return
-		
-		fd.incparentsf1 = 1
-		if not fd.genotype:
-			fd.readGenotype()
-
-		locusChr = {}
-		locusMb = {}
-		for chr in fd.genotype:
-			for locus in chr:
-				locusChr[locus.name] = locus.chr
-				locusMb[locus.name] = locus.Mb
-				
-		self.searchResult = fd.formdata.getvalue('searchResult')
-		
-		if not self.searchResult:
-			templatePage.__init__(self, fd)
-			heading = 'Export Collection'
-			detail = ['You need to select at least one trait to export.']
-			self.error(heading=heading,detail=detail)
-			return
-			
-		self.RISet = fd.formdata.getvalue("RISet")	
-		self.cursor.execute("Select Species.Name from Species, InbredSet where InbredSet.SpeciesId = Species.Id and InbredSet.Name = '%s'" % self.RISet)
-		self.Species = self.cursor.fetchone()[0]
-		
-		if type("1") == type(self.searchResult):
-			self.searchResult = string.split(self.searchResult,'\t')
-		strainlist = fd.f1list + fd.strainlist
-		fields = ["ID", "Species", "Cross", "Database", "ProbeSetID / RecordID", "Symbol", "Description", "ProbeTarget", "PubMed_ID", "Phenotype", "Chr", "Mb", "Alias", "Gene_ID", "HomoloGene_ID", "UniGene_ID", "Strand_Probe ", "Strand_Gene ", "Probe_set_specificity", "Probe_set_BLAT_score", "Probe_set_BLAT_Mb_start", "Probe_set_BLAT_Mb_end ", "QTL_Chr", "QTL_Mb", "Locus_at_Peak", "Max_LRS", "P_value_of_MAX", "Mean_Expression"] + strainlist
-		
-		if self.searchResult:
-			traitList = []
-			for item in self.searchResult:
-				thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-				thisTrait.retrieveInfo(QTL=1)
-				thisTrait.retrieveData(strainlist=strainlist)
-				traitList.append(thisTrait)
-
-			text = [fields]
-			for i, thisTrait in enumerate(traitList):
-				if thisTrait.db.type == 'ProbeSet':
-					if not thisTrait.cellid: #ProbeSet
-						#12/22/2009, XZ: We calculated LRS for each marker(locus) in geno file and record the max LRS and its corresponding marker in MySQL database. But after the calculation, Rob deleted several markers. If one of the deleted markers happen to be the one recorded in database, error will occur. So we have to deal with this situation.
-						if locusChr.has_key(thisTrait.locus) and locusMb.has_key(thisTrait.locus):
-							text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, locusChr[thisTrait.locus], locusMb[thisTrait.locus], thisTrait.locus, thisTrait.lrs, thisTrait.pvalue])
-						else:
-                                                        text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, thisTrait.strand_probe, thisTrait.strand_gene, thisTrait.probe_set_specificity, thisTrait.probe_set_blat_score, thisTrait.probe_set_blat_mb_start, thisTrait.probe_set_blat_mb_end, "", "", "", "", ""])
-                                        else: #Probe
-                                                text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name + " : " + thisTrait.cellid, thisTrait.symbol, thisTrait.description, thisTrait.probe_target_description,"", "", thisTrait.chr, thisTrait.mb, thisTrait.alias, thisTrait.geneid, thisTrait.homologeneid, thisTrait.unigeneid, "", "", "", "", "", "", "", "", "", "", ""])
-
-				elif thisTrait.db.type == 'Publish':
-					#XZ: need to consider confidential phenotype
-					PhenotypeString = thisTrait.post_publication_description
-					if thisTrait.confidential:
-						if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=thisTrait.authorized_users):
-							PhenotypeString = thisTrait.pre_publication_description
-					text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", "", "", thisTrait.pubmed_id, PhenotypeString, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
-				elif thisTrait.db.type == 'Temp':
-					text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.description, "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "","", ""])
-				elif thisTrait.db.type == 'Geno':
-					text.append([str(i+1), self.Species, self.RISet, thisTrait.db.fullname, thisTrait.name, "", thisTrait.name,"", "", "", thisTrait.chr, thisTrait.mb, "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""])
-				else:
-					continue
-				
-				testval = thisTrait.exportData(strainlist)
-				try:
-					mean = reaper.anova(testval)[0]
-				except:
-					count = 0
-					sum = 0
-					for oneValue in testval:
-						try:
-							oneValue = float(oneValue)
-							sum = sum + oneValue
-							count = count + 1
-						except:
-							pass
-					if count == 0:
-						mean = 0
-					else:
-						mean = sum/count
-				text[-1].append(mean)
-				text[-1] += testval
-			if len(text[0]) < 255 or len(text) < 255:
-				transpose = 0
-				if len(text[0]) >= 255:
-					text = webqtlUtil.transpose(text)
-					transpose = 1
-				filename = os.path.join(webqtlConfig.TMPDIR, webqtlUtil.generate_session() +'.xls')
-							
-				# Create a new Excel workbook
-				workbook = xl.Writer(filename)
-				worksheet = workbook.add_worksheet()
-				headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, color = 'green')
-				titleStyle = workbook.add_format(align = 'left', bold = 0, size=13, border = 1, border_color="gray")
-				
-				##Write title Info
-				# Modified by Hongqiang Li
-				# worksheet.write([0, 0], "Data source: The GeneNetwork at web2qtl.utmem.edu:88", titleStyle)
-				# worksheet.write([1, 0], "Citations: Please see web2qtl.utmem.edu:88/reference.html", titleStyle)
-				worksheet.write([0, 0], "Data source: The GeneNetwork at %s" % webqtlConfig.PORTADDR, titleStyle)
-				worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
-				#
-				worksheet.write([2, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
-				worksheet.write([3, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
-			
-				# Modified by Hongqiang Li	
-				# worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see web2qtl.utmem.edu:88/statusandContact.html for details on sources, ownership, and usage of these data.", titleStyle)
-				worksheet.write([4, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
-				#
-				worksheet.write([6, 0], "This output file contains data from %d GeneNetwork databases listed below" % len(traitList), titleStyle)
-			
-				# Row and column are zero indexed
-				nrow = startRow = 8
-				for row in text:
-				    for ncol, cell in enumerate(row):
-				    	if nrow == startRow:
-				        	worksheet.write([nrow, ncol], cell.strip(), headingStyle)
-				        	worksheet.set_column([ncol, ncol], 2*len(cell))
-				    	else:
-				        	worksheet.write([nrow, ncol], cell)
-				    nrow += 1
-				
-				worksheet.write([nrow+1, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA 21131), NCI MMHCC (U01CA105417), and NCRR (U24 RR021760)", titleStyle)
-				worksheet.write([nrow+2, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
-				workbook.close()
-								
-				fp = open(filename, 'rb')
-				text = fp.read()
-				fp.close()
-				
-				self.content_type = 'application/xls'
-				self.content_disposition = 'attachment; filename=%s' % ('export-%s.xls' % time.strftime("%y-%m-%d-%H-%M"))
-				self.attachment = text
-			else:
-				self.content_type = 'application/xls'
-				self.content_disposition = 'attachment; filename=%s' % ('export-%s.txt' % time.strftime("%y-%m-%d-%H-%M"))
-				for item in text:
-					self.attachment += string.join(map(str, item), '\t')+ "\n"
-			self.cursor.close()
-		else:
-			fd.req.content_type = 'text/html'
-			heading = 'Export Collection'
-			detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
-			self.error(heading=heading,detail=detail)
-			
-