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

1 files changed, 0 insertions, 335 deletions

diff --git a/web/webqtl/networkGraph/networkGraphPage.py b/web/webqtl/networkGraph/networkGraphPage.py
deleted file mode 100755
index fb4021f0..00000000
--- a/web/webqtl/networkGraph/networkGraphPage.py
+++ /dev/null
@@ -1,335 +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 NL 2010/02/11
-
-#!/usr/bin/python
-# networkGraph.py
-# Author: Stephen Pitts
-# 6/2/2004
-#
-# a script to take a matrix of data from a WebQTL job and generate a
-# graph using the neato package from GraphViz
-#
-# See graphviz for documentation of the parameters
-#
-
-
-#from mod_python import apache, util, Cookie
-#import cgi
-import tempfile
-import os
-import time
-import sys
-import cgitb
-import string
-
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-import networkGraphUtils
-from base import webqtlConfig
-from utility import webqtlUtil
-from base.webqtlTrait import webqtlTrait
-import compareCorrelates.trait as smpTrait
-from GraphPage import GraphPage
-from networkGraphPageBody import networkGraphPageBody
-from correlationMatrix.tissueCorrelationMatrix import tissueCorrelationMatrix
-
-cgitb.enable()
-
-
-class networkGraphPage(templatePage):
-
-    def __init__(self,fd,InputData=None):
-
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-            return
-            
-        if not fd.genotype:
-            fd.readGenotype()
-                
-        self.searchResult = fd.formdata.getvalue('searchResult')
-
-        self.tissueProbeSetFeezeId = "1" #XZ, Jan 03, 2010: currently, this dataset is "UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)"
-        TissueCorrMatrixObject = tissueCorrelationMatrix(tissueProbeSetFreezeId=self.tissueProbeSetFeezeId)
-
-        if type("1") == type(self.searchResult):
-            self.searchResult = string.split(self.searchResult, '\t')
-        
-        if (not self.searchResult or (len(self.searchResult) < 2)):
-            heading = 'Network Graph'
-            detail = ['You need to select at least two traits in order to generate Network Graph.']
-            self.error(heading=heading,detail=detail)
-            print 'Content-type: text/html\n'
-            self.write()
-            return
-        
-        if self.searchResult:
-            if len(self.searchResult) > webqtlConfig.MAXCORR:
-                heading = 'Network Graph'
-                detail = ['In order to display Network Graph properly, Do not select more than %d traits for Network Graph.' % webqtlConfig.MAXCORR]
-                self.error(heading=heading,detail=detail)
-                print 'Content-type: text/html\n'
-                self.write()
-                return
-            else:    
-                pass
-                
-            traitList = []
-            traitDataList = []
-            
-            for item in self.searchResult:
-                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-                thisTrait.retrieveInfo()
-                thisTrait.retrieveData(fd.strainlist)
-                traitList.append(thisTrait)
-                traitDataList.append(thisTrait.exportData(fd.strainlist))
-                   
-        else:
-            heading = 'Network Graph'
-            detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
-            self.error(heading=heading,detail=detail)
-            print 'Content-type: text/html\n'
-            self.write()
-            return
-
-        NNN = len(traitList)
-        
-        if NNN < 2:
-            templatePage.__init__(self, fd)
-            heading = 'Network Graph'
-            detail = ['You need to select at least two traits in order to generate a Network Graph']
-            print 'Content-type: text/html\n'
-            self.write()
-            return
-        else:
-            pearsonArray = [([0] * (NNN))[:] for i in range(NNN)]
-            spearmanArray = [([0] * (NNN))[:] for i in range(NNN)]
-            GeneIdArray = []
-            GeneSymbolList = [] #XZ, Jan 03, 2011: holds gene symbols for calculating tissue correlation
-            traitInfoArray = []
-
-            i = 0
-            nnCorr = len(fd.strainlist)
-            for i, thisTrait in enumerate(traitList):
-                names1 = [thisTrait.db.name, thisTrait.name, thisTrait.cellid]
-                for j, thisTrait2 in enumerate(traitList):
-                    names2 = [thisTrait2.db.name, thisTrait2.name, thisTrait2.cellid]
-                    if j < i:
-                        corr,nOverlap = webqtlUtil.calCorrelation(traitDataList[i],traitDataList[j],nnCorr)
-                        pearsonArray[i][j] = corr
-                        pearsonArray[j][i] = corr
-                    elif j == i:
-                        pearsonArray[i][j] = 1.0
-                        spearmanArray[i][j] = 1.0
-                    else:
-                        corr,nOverlap = webqtlUtil.calCorrelationRank(traitDataList[i],traitDataList[j],nnCorr)
-                        spearmanArray[i][j] = corr
-                        spearmanArray[j][i] = corr
-                    
-                GeneId1 = None
-                tmpSymbol = None
-                if thisTrait.db.type == 'ProbeSet':
-                    try:
-                        GeneId1 = int(thisTrait.geneid)
-                    except:
-                        GeneId1 = 0
-                    if thisTrait.symbol:
-                        tmpSymbol = thisTrait.symbol.lower()
-                GeneIdArray.append(GeneId1)
-                GeneSymbolList.append(tmpSymbol)
-
-            _traits = []
-            _matrix = []
-
-            for i in range(NNN):
-                turl = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s&ProbeSetID=%s' % (traitList[i].db.name, traitList[i].name)
-                if traitList[i].cellid:
-                    turl += "&CellID=%s" % traitList[i].cellid
-                    
-                if traitList[i].db.type == 'ProbeSet':
-                    if traitList[i].symbol:
-                        _symbol = traitList[i].symbol
-                    else:
-                        _symbol = 'unknown'
-                elif traitList[i].db.type == 'Publish':
-                    _symbol = traitList[i].name
-                    if traitList[i].confidential:
-                        if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=traitList[i].authorized_users):
-                            if traitList[i].post_publication_abbreviation:
-                                _symbol = traitList[i].post_publication_abbreviation
-                        else:
-                            if traitList[i].pre_publication_abbreviation:
-                                _symbol = traitList[i].pre_publication_abbreviation
-                    else:
-                        if traitList[i].post_publication_abbreviation:
-                            _symbol = traitList[i].post_publication_abbreviation
-
-                #XZ, 05/26/2009: Xiaodong add code for Geno data
-                elif traitList[i].db.type == 'Geno':
-                    _symbol = traitList[i].name
-                else:
-                    _symbol = traitList[i].description
-                    #####if this trait entered by user
-                    if _symbol.__contains__('entered'):
-                        _symbol = _symbol[:_symbol.index('entered')]
-                    #####if this trait generaged by genenetwork
-                    elif _symbol.__contains__('generated'):
-                        _symbol = _symbol[_symbol.rindex(':')+1:]
-                
-                newTrait = smpTrait.Trait(name=str(traitList[i]), href=turl, symbol=_symbol)
-                newTrait.color = "black"
-                _traits.append(newTrait)
-                
-                for j in range(i+1, NNN):
-                    dataPoint = smpTrait.RawPoint(i, j)
-                    dataPoint.spearman = spearmanArray[i][j]
-                    dataPoint.pearson = pearsonArray[i][j]
-
-                    #XZ: get literature correlation info.
-                    if GeneIdArray[i] and GeneIdArray[j]:
-                        if GeneIdArray[i] == GeneIdArray[j]:
-                            dataPoint.literature = 1
-                        else:
-                            self.cursor.execute("SELECT Value from LCorrRamin3 WHERE (GeneId1 = %d and GeneId2 = %d) or (GeneId1 = %d and GeneId2 = %d)" % (GeneIdArray[i], GeneIdArray[j], GeneIdArray[j], GeneIdArray[i]))
-                            try:    
-                                dataPoint.literature = self.cursor.fetchone()[0]
-                            except:
-                                dataPoint.literature = 0
-                    else:
-                        dataPoint.literature = 0
-
-                    #XZ: get tissue correlation info
-                    if GeneSymbolList[i] and GeneSymbolList[j]:
-                        dataPoint.tissue = 0
-                        geneSymbolPair = []
-                        geneSymbolPair.append(GeneSymbolList[i])
-                        geneSymbolPair.append(GeneSymbolList[j])
-                        corrArray,pvArray = TissueCorrMatrixObject.getCorrPvArrayForGeneSymbolPair(geneNameLst=geneSymbolPair)
-                        if corrArray[1][0]:
-                            dataPoint.tissue = corrArray[1][0]
-                    else:
-                        dataPoint.tissue = 0
-
-                    _matrix.append(dataPoint)
-        
-            OrigDir = os.getcwd()
-
-            sessionfile = fd.formdata.getvalue('session')
-            
-            inputFilename = fd.formdata.getvalue('inputFile')
-
-            #If there is no sessionfile generate one and dump all matrix/trait values
-            if not sessionfile:
-                filename = webqtlUtil.generate_session()    
-                webqtlUtil.dump_session([_matrix, _traits], os.path.join(webqtlConfig.TMPDIR, filename + '.session'))
-                sessionfile = filename
-            
-            startTime = time.time()
-            
-            #Build parameter dictionary used by networkGraphPage class using buildParamDict function
-            params = networkGraphUtils.buildParamDict(fd, sessionfile)
-    
-            nodes = len(_traits)
-            rawEdges = len(_matrix)
-            
-            if params["tune"] == "yes":
-                params = networkGraphUtils.tuneParamDict(params, nodes, rawEdges)
-              
-            matrix = networkGraphUtils.filterDataMatrix(_matrix, params)
-            
-            optimalNode = networkGraphUtils.optimalRadialNode(matrix)
-            
-            if not inputFilename:
-                inputFilename = tempfile.mktemp()
-            
-            inputFilename = webqtlConfig.IMGDIR + inputFilename.split("/")[2]
-                                           
-            #writes out 4 graph files for exporting
-            graphFile = "/image/" + networkGraphUtils.writeGraphFile(matrix, _traits, inputFilename, params)
-            
-            networkGraphUtils.processDataMatrix(matrix, params)
-
-            edges = 0
-
-            for edge in matrix:
-                if edge.value != 0:
-                    edges +=1
-
-            for trait in _traits:
-                trait.name = networkGraphUtils.fixLabel(trait.name)
-            
-            RootDir = webqtlConfig.IMGDIR
-            RootDirURL = "/image/"                  
-
-
-                  
-                        #This code writes the datafile that the graphviz function runNeato uses to generate the 
-                        #"digraph" file that defines the graphs parameters
-            datafile = networkGraphUtils.writeNeatoFile(matrix=matrix, traits=_traits, filename=inputFilename, GeneIdArray=GeneIdArray, p=params)
-            
-            #Generate graph in various file types                      
-            layoutfile = networkGraphUtils.runNeato(datafile, "dot", "dot", params["gType"]) # XZ, 09/11/2008: add module name
-            # ZS 03/04/2010 This second output file (layoutfile_pdf) is rotated by 90 degrees to prevent an issue with pdf output being cut off at the edges
-            layoutfile_pdf = networkGraphUtils.runNeato(datafile + "_pdf", "dot", "dot", params["gType"]) # ZS 03/04/2010
-            pngfile = networkGraphUtils.runNeato(layoutfile, "png", "png", params["gType"]) 
-            mapfile = networkGraphUtils.runNeato(layoutfile, "cmapx", "cmapx", params["gType"])# XZ, 09/11/2008: add module name    
-            giffile = networkGraphUtils.runNeato(layoutfile, "gif", "gif", params["gType"])# XZ, 09/11/2008:add module name
-            psfile = networkGraphUtils.runNeato(layoutfile_pdf, "ps", "ps", params["gType"])# XZ, 09/11/2008: add module name
-            pdffile = networkGraphUtils.runPsToPdf(psfile, params["width"], params["height"])# XZ, 09/11/2008: add module name
-            
-                        #This generates text files in XGGML (standardized graphing language) and plain text
-                        #so the user can create his/her own graphs in a program like Cytoscape
-                    
-            htmlfile1 = datafile + ".html"
-            htmlfile2 = datafile + ".graph.html"
-
-            os.chdir(OrigDir)
-
-            #This generates the graph in various image formats
-            giffile = RootDirURL + giffile
-            pngfile = RootDirURL + pngfile
-            pdffile = RootDirURL + pdffile
-            endTime = time.time()
-            totalTime = endTime - startTime
-
-            os.chdir(RootDir)
-
-            page2 = GraphPage(giffile, mapfile)
-            page2.writeToFile(htmlfile2)
-            
-            #This generates the HTML for the body of the Network Graph page
-            page1 = networkGraphPageBody(fd, matrix, _traits, htmlfile2, giffile, pdffile, nodes, edges, rawEdges, totalTime, params, page2.content, graphFile, optimalNode)
-            
-            #Adds the javascript colorSel to the body to allow line color selection
-            self.dict["js1"] = '<SCRIPT SRC="/javascript/colorSel.js"></SCRIPT><BR>'   
-            #self.dict["js1"] += '<SCRIPT SRC="/javascript/networkGraph.js"></SCRIPT>' 
-                        
-            #Set body of current templatePage to body of the templatePage networkGraphPage                        
-            self.dict['body'] = page1.dict['body']                
-
-