Add all the source codes into the github.

1 files changed, 335 insertions, 0 deletions

diff --git a/web/webqtl/networkGraph/networkGraphPage.py b/web/webqtl/networkGraph/networkGraphPage.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 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']                
+
+