diff options
Diffstat (limited to 'web/webqtl/maintainance')
| -rwxr-xr-x | web/webqtl/maintainance/__init__.py | 0 | ||||
| -rwxr-xr-x | web/webqtl/maintainance/addRif.py | 107 | ||||
| -rwxr-xr-x | web/webqtl/maintainance/checkInfoFile.py | 102 | ||||
| -rwxr-xr-x | web/webqtl/maintainance/genSelectDatasetJS.py | 637 | ||||
| -rwxr-xr-x | web/webqtl/maintainance/updateMenuJS.py | 127 |
5 files changed, 973 insertions, 0 deletions
diff --git a/web/webqtl/maintainance/__init__.py b/web/webqtl/maintainance/__init__.py new file mode 100755 index 00000000..e69de29b --- /dev/null +++ b/web/webqtl/maintainance/__init__.py diff --git a/web/webqtl/maintainance/addRif.py b/web/webqtl/maintainance/addRif.py new file mode 100755 index 00000000..c7cdde7a --- /dev/null +++ b/web/webqtl/maintainance/addRif.py @@ -0,0 +1,107 @@ +# 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 Lei Yan 2011/02/08 + +# created by Lei Yan 02/08/2011 + +import string +import MySQLdb +import time +import os +import sys + +path1 = os.path.abspath(os.path.dirname(__file__)) +path2 = path1 + "/.." +path3 = path1 + "/../../tmp" +sys.path.insert(0, path2) +from base import webqtlConfig + +try: + con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) + cursor = con.cursor() + print "You have successfully connected to mysql.\n" +except: + print "You entered incorrect password.\n" + sys.exit(0) + +taxIds = {'10090':1, '9606':4, '10116':2, '3702':3} +taxIdKeys = taxIds.keys() + +os.chdir(path3) +cdict = {} + +os.system("rm -f gene_info") +os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz") +os.system("gunzip gene_info.gz") +try: + fp = open("gene_info") +except: + print "gene_info doesn't exit" + sys.exit(1) + +i=0 +line = fp.readline() +while line: + line2 = map(string.strip, string.split(line.strip(), "\t")) + if line2[0] in taxIdKeys: + cdict[line2[1]] = line2[2] + line = fp.readline() + i += 1 + if i%1000 == 0: + print "finished ", i +fp.close() + +os.system("rm -f generifs_basic") +os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/generifs_basic.gz") +os.system("gunzip generifs_basic.gz") +try: + fp = open("generifs_basic") +except: + print "generifs_basic doesn't exist" + sys.exit(1) + +cursor.execute("delete from GeneRIF_BASIC") +count = 0 +line = fp.readline() +while line: + line2 = map(string.strip, string.split(line.strip(), "\t")) + if line2[0] in taxIdKeys: + count += 1 + line2[0] = taxIds[line2[0]] + if len(line2) !=5: + print line + else: + try: + symbol=cdict[line2[1]] + except: + symbol= "" + + line2 = line2[:2] + [symbol] + line2[2:] + cursor.execute("insert into GeneRIF_BASIC(SpeciesId, GeneId, Symbol, PubMed_ID, createtime, comment) values(%s, %s, %s, %s, %s, %s)", tuple(line2)) + line = fp.readline() + +fp.close() +print count, "\n" +cursor.close() diff --git a/web/webqtl/maintainance/checkInfoFile.py b/web/webqtl/maintainance/checkInfoFile.py new file mode 100755 index 00000000..6aa0d771 --- /dev/null +++ b/web/webqtl/maintainance/checkInfoFile.py @@ -0,0 +1,102 @@ +# 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 2011/01/28 + +# created by Ning Liu 2011/01/27 +# This script is to check whether dataset related Info file exist or not; if not, the tempate Info file will be generated +# This script should be only run at GeneNetwork production server + +import sys, os +import MySQLdb + +current_file_name = __file__ +pathname = os.path.dirname( current_file_name ) +abs_path = os.path.abspath(pathname) +sys.path.insert(0, abs_path + '/..') + +from base import template +from base import webqtlConfig +from base import header +from base import footer + +# build MySql database connection +con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) +cursor = con.cursor() + +InfoFilePath =webqtlConfig.HTMLPATH+'dbdoc/' + +# create template for Info file +def createTemplateForInfoFile(datasetId=None,datasetFullName=None,InfoFileURL=None): + #template.py has been changed with dynamic header and footer + userInfo="" + headerInfo=header.header_string % userInfo + serverInfo="" + footerInfo=footer.footer_string % serverInfo + + title =datasetFullName + contentTitle = ''' + <P class="title">%s<A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR> + ''' % datasetFullName + content =''' + Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s">GN%s</A></P> + <br><br> + This page will be updated soon. + <br><br> + ''' % (datasetId,datasetId) + + body=contentTitle+content + # Note: 'templateParameters' includes parameters required for template.py + # templateParameters = ['title','basehref','js1','js2','layer','header','body', 'footer'] + templateParameters =[title,'','','','',headerInfo,body,footerInfo] + + # build template file + templateFile=template.template % tuple(templateParameters) + InfoFileHandler = open(InfoFileURL, 'w') + # write template file into Info .html file + InfoFileHandler.write(templateFile) + InfoFileHandler.close() + + +# select all ProbeSet names from datatable 'ProbeSetFreeze' +cursor.execute("select Id, Name, FullName from ProbeSetFreeze ") +results = cursor.fetchall() +for item in results: + datasetId = item[0] + datasetName =item[1] + datasetFullName =item[2] + InfoFileURL = InfoFilePath+datasetName+".html" + # check Info html file exist or not + if not os.path.exists(InfoFileURL): + createTemplateForInfoFile(datasetId=datasetId,datasetFullName=datasetFullName,InfoFileURL=InfoFileURL) + + + + + + + + + + diff --git a/web/webqtl/maintainance/genSelectDatasetJS.py b/web/webqtl/maintainance/genSelectDatasetJS.py new file mode 100755 index 00000000..bc88beec --- /dev/null +++ b/web/webqtl/maintainance/genSelectDatasetJS.py @@ -0,0 +1,637 @@ +# 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 2011/01/27 + +# created by Ning Liu 07/01/2010 +# This script is to generate selectDatasetMenu.js file for cascade menu in the main search page http://www.genenetwork.org/. +# This script will be run automatically every one hour or manually when database has been changed . +import sys, os + +current_file_name = __file__ +pathname = os.path.dirname( current_file_name ) +abs_path = os.path.abspath(pathname) +sys.path.insert(0, abs_path + '/..') + +import MySQLdb +import os +import string +import time +import datetime + +from base import template +from base import webqtlConfig + +################################################################################# +# input: searchArray, targetValue +# function: retrieve index info of target value in designated array (searchArray) +# output: return index info +################################################################################## +def getIndex(searchArray=None, targetValue=None): + for index in range(len(searchArray)): + if searchArray[index][0]==targetValue: + return index + +# build MySql database connection +con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) +cursor = con.cursor() + +# create js_select.js file +fileHandler = open(webqtlConfig.HTMLPATH + 'javascript/selectDatasetMenu.js', 'w') + +# define SpeciesString, GroupString, TypeString, DatabasingString, LinkageString for output +# outputSpeciesStr is for building Species Array(sArr) in js file; outputGroupStr is for Group Array(gArr) +# outputTypeStr is for Type Array(tArr); outputDatabaseStr is for Database Array(dArr) +# outputLinkStr is for Linkage Array(lArr) +outputTimeStr ="/* Generated Date : %s , Time : %s */ \n" % (datetime.date.today(),time.strftime("%H:%M ", time.localtime())) +outputTimeStr ="" +outputSpeciesStr ='var sArr = [\n{txt:\'\',val:\'\'},\n' +outputGroupStr ='var gArr = [\n{txt:\'\',val:\'\'},\n' +outputTypeStr ='var tArr = [\n{txt:\'\',val:\'\'},\n' +outputDatabaseStr ='var dArr = [\n{txt:\'\',val:\'\'},\n' +outputLinkStr ='var lArr = [\n null,\n' + +# built speices array in js file for select menu in the main search page http://www.genenetwork.org/ +cursor.execute("select Name, MenuName from Species order by OrderId") +speciesResult = cursor.fetchall() +speciesTotalResult = list(speciesResult) +speciesResultsTotalNum = cursor.rowcount +if speciesResultsTotalNum >0: + for speciesItem in speciesResult: + speciesVal = speciesItem[0] + speciesTxt = speciesItem[1] + outputSpeciesStr += '{txt:\'%s\',val:\'%s\'},\n'%(speciesTxt,speciesVal) +# 'All Species' option for 'Species' select menu +outputSpeciesStr +='{txt:\'All Species\',val:\'All Species\'}];\n\n' +#speciesTotalResult is a list which inclues all species' options +speciesTotalResult.append(('All Species','All Species')) + +# built group array in js file for select menu in the main search page http://www.genenetwork.org/ +cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name") +groupResults = cursor.fetchall() +groupTotalResults = list(groupResults) +groupResultsTotalNum = cursor.rowcount +if groupResultsTotalNum > 0: + for groupItem in groupResults: + groupVal = groupItem[0] + groupTxt = groupItem[1] + outputGroupStr += '{txt:\'%s\',val:\'%s\'},\n'%(groupTxt,groupVal) +# add 'All Groups' option for 'Group' select menu +outputGroupStr +='{txt:\'All Groups\',val:\'all groups\'}];\n\n' +# groupTotalResults is a list which inclues all groups' options +groupTotalResults.append(('all groups','All Groups')) + +# built type array in js file for select menu in the main search page http://www.genenetwork.org/ +cross = groupVal +cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (webqtlConfig.PUBLICTHRESH)) +typeResults = cursor.fetchall() +typeTotalResults = list(typeResults) +typeResultsTotalNum = cursor.rowcount +if typeResultsTotalNum > 0: + for typeItem in typeResults: + typeVal = typeItem[0] + typeTxt = typeItem[1] + outputTypeStr += '{txt:\'%s\',val:\'%s\'},\n'%(typeTxt,typeVal) +# add 'Phenotypes' and 'Genotypes' options for 'Type' select menu +outputTypeStr +='{txt:\'Phenotypes\',val:\'Phenotypes\'},\n' +outputTypeStr +='{txt:\'Genotypes\',val:\'Genotypes\'}];\n\n' +# typeTotalResults is a list which inclues all types' options +typeTotalResults.append(('Phenotypes','Phenotypes')) +typeTotalResults.append(('Genotypes','Genotypes')) + +# built dataset array in js file for select menu in the main search page http://www.genenetwork.org/ +tissue = typeVal +cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (webqtlConfig.PUBLICTHRESH)) +datasetResults = cursor.fetchall() +datasetTotalResults = list(datasetResults) +datasetResultsTotalNum = cursor.rowcount +if datasetResultsTotalNum > 0: + for datasetItem in datasetResults: + datasetVal = datasetItem[0] + datasetTxt = datasetItem[1] + outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal) + +# This part is to built linkage array in js file, the linkage is among Species, Group, Type and Database. +# The format of linkage array is [speciesIndex, groupIndex, typeIndex, databaseIndex] +if speciesResultsTotalNum >0: + for speciesItem in speciesResult: + speciesVal = speciesItem[0] + sIndex = getIndex(searchArray=speciesTotalResult,targetValue=speciesVal)+1 + + # retrieve group info based on specie + cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name" % speciesVal) + groupResults = cursor.fetchall() + groupResultsNum = cursor.rowcount + + if groupResultsNum > 0: + for groupItem in groupResults: + groupVal = groupItem[0] + gIndex = getIndex(searchArray=groupTotalResults, targetValue=groupVal)+1 + + cross = groupVal + # if group also exists in PublishFreeze table, then needs to add related Published Phenotypes in Database Array(dArr) and Linkage Array(lArr) + # 'MDP' case is related to 'Mouse Phenome Database' + cursor.execute("select PublishFreeze.Id from PublishFreeze, InbredSet where PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross) + if (cursor.fetchall()): + typeVal = "Phenotypes" + if cross=='MDP': + datasetTxt = "Mouse Phenome Database" + else: + datasetTxt = "%s Published Phenotypes" % cross + datasetVal = "%sPublish" % cross + outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'% (datasetTxt,datasetVal) + datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) + + tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1 + dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 + outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) + + # if group also exists in GenoFreeze table, then needs to add related Genotypes in database Array(dArr) + cursor.execute("select GenoFreeze.Id from GenoFreeze, InbredSet where GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross) + if (cursor.fetchall()): + typeVal = "Genotypes" + datasetTxt = "%s Genotypes" % cross + datasetVal = "%sGeno" % cross + outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal) + typeTotalResults.append(('Genotypes','Genotypes')) + datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) + + tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1 + dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 + outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) + + # retrieve type(tissue) info based on group + # if cross is equal to 'BXD', then need to seach for 'BXD' and 'BXD300' InbredSet + if cross == "BXD": + cross2 = "BXD', 'BXD300" + else: + cross2 = cross + cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (cross2, webqtlConfig.PUBLICTHRESH)) + typeResults = cursor.fetchall() + typeResultsNum = cursor.rowcount + + if typeResultsNum > 0: + for typeItem in typeResults: + typeVal = typeItem[0] + tIndex = getIndex(searchArray=typeTotalResults, targetValue=typeVal)+1 + # retrieve database(dataset) info based on group(InbredSet) and type(Tissue) + tissue = typeVal + cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (cross2, tissue, webqtlConfig.PUBLICTHRESH)) + datasetResults = cursor.fetchall() + datasetResultsNum = cursor.rowcount + + if datasetResultsNum > 0: + for datasetItem in datasetResults: + datasetVal = datasetItem[0] + dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 + outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) + +# add 'All Phenotypes' option for 'Database' select menu +# for 'All Species'option in 'Species' select menu, 'Database' select menu will show 'All Phenotypes' option +outputDatabaseStr += '{txt:\'%s\',val:\'%s\'}];\n\n'%('All Phenotypes','_allPublish') +datasetTotalResults.append(('_allPublish','All Phenotypes')) + +sIndex = getIndex(searchArray=speciesTotalResult,targetValue='All Species')+1 +gIndex = getIndex(searchArray=groupTotalResults, targetValue='all groups')+1 +tIndex = getIndex(searchArray=typeTotalResults,targetValue='Phenotypes')+1 +dIndex = getIndex(searchArray=datasetTotalResults, targetValue='_allPublish')+1 +outputLinkStr +='[%d,%d,%d,%d]];\n\n'%(sIndex,gIndex,tIndex,dIndex) + +# Combine sArr, gArr, tArr, dArr and lArr output string together +outputStr = outputTimeStr+outputSpeciesStr+outputGroupStr+outputTypeStr+outputDatabaseStr+outputLinkStr +outputStr +=''' + +/* +* function: based on different browser use, will have different initial actions; +* Once the index.html page is loaded, this function will be called +*/ +function initialDatasetSelection() +{ + defaultSpecies =getDefaultValue('species'); + defaultSet =getDefaultValue('cross'); + defaultType =getDefaultValue('tissue'); + defaultDB =getDefaultValue('database'); + + if (navigator.userAgent.indexOf('MSIE')>=0) + { + sOptions = fillOptionsForIE(null,defaultSpecies); + var menu0 ="<SELECT NAME='species' ID='species' SIZE='1' onChange='fillOptions(\\"species\\");'>"+sOptions+"</Select>"; + document.getElementById('menu0').innerHTML = menu0; + + gOptions = fillOptionsForIE('species',defaultSet); + var menu1 ="<Select NAME='cross' size=1 id='cross' onchange='fillOptions(\\"cross\\");'>"+gOptions+"</Select><input type=\\"button\\" class=\\"button\\" value=\\"Info\\" onCLick=\\"javascript:crossinfo();\\">"; + document.getElementById('menu1').innerHTML =menu1; + + tOptions = fillOptionsForIE('cross',defaultType); + var menu2 ="<Select NAME='tissue' size=1 id='tissue' onchange='fillOptions(\\"tissue\\");'>"+tOptions+"</Select>"; + document.getElementById('menu2').innerHTML =menu2; + + dOptions = fillOptionsForIE('tissue',defaultDB); + var menu3 ="<Select NAME='database' size=1 id='database'>"+dOptions+"</Select><input type=\\"button\\" class=\\"button\\" value=\\"Info\\" onCLick=\\"javascript:databaseinfo();\\">"; + document.getElementById('menu3').innerHTML =menu3; + + }else{ + fillOptions(null); + } + searchtip(); +} + +/* +* input: selectObjId (designated select menu, such as species, cross, etc... ) +* defaultValue (default Value of species, cross,tissue or database) +* function: special for IE browser,setting options value for select menu dynamically based on linkage array(lArr), +* output: options string +*/ +function fillOptionsForIE(selectObjId,defaultValue) +{ + var options=''; + if(selectObjId==null) + { + var len = sArr.length; + for (var i=1; i < len; i++) { + // setting Species' option + if( sArr[i].val==defaultValue){ + options =options+"<option selected=\\"selected\\" value='"+sArr[i].val+"'>"+sArr[i].txt+"</option>"; + }else{ + options =options+"<option value='"+sArr[i].val+"'>"+sArr[i].txt+"</option>"; + } + } + }else if(selectObjId=='species') + { + var speciesObj = document.getElementById('species'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get group(cross) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1])) + { + arr[idx++]=lArr[i][1]; + } + } + idx=0; + len = arr.length; + removeOptions("cross"); + for (var i=0; i < len; i++) { + // setting Group's option + if( gArr[arr[i]].val==defaultValue){ + options =options+"<option selected=\\"selected\\" value='"+gArr[arr[i]].val+"'>"+gArr[arr[i]].txt+"</option>"; + }else{ + options =options+"<option value='"+gArr[arr[i]].val+"'>"+gArr[arr[i]].txt+"</option>"; + } + + } + }else if(selectObjId=='cross') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get type(tissue) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2])) + { + arr[idx++]=lArr[i][2]; + } + } + idx=0; + len = arr.length; + removeOptions("tissue"); + for (var i=0; i < len; i++) { + // setting Type's option + if( tArr[arr[i]].val==defaultValue){ + options =options+"<option selected=\\"selected\\" value='"+tArr[arr[i]].val+"'>"+tArr[arr[i]].txt+"</option>"; + }else{ + options =options+"<option value='"+tArr[arr[i]].val+"'>"+tArr[arr[i]].txt+"</option>"; + } + } + + }else if(selectObjId=='tissue') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var typeObj = document.getElementById('tissue'); + + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get dataset(database) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3])) + { + arr[idx++]=lArr[i][3]; + } + } + idx=0; + len = arr.length; + removeOptions("database"); + for (var i=0; i < len; i++) { + // setting Database's option + if( dArr[arr[i]].val==defaultValue){ + options =options+"<option SELECTED value='"+dArr[arr[i]].val+"'>"+dArr[arr[i]].txt+"</option>"; + }else{ + options =options+"<option value='"+dArr[arr[i]].val+"'>"+dArr[arr[i]].txt+"</option>"; + } + } + } + return options; +} +/* +* input: selectObjId (designated select menu, such as species, cross, etc... ) +* function: setting options value for select menu dynamically based on linkage array(lArr) +* output: null +*/ +function fillOptions(selectObjId) +{ + if(selectObjId==null) + { + + var speciesObj = document.getElementById('species'); + var len = sArr.length; + for (var i=1; i < len; i++) { + // setting Species' option + speciesObj.options[i-1] = new Option(sArr[i].txt, sArr[i].val); + } + updateChocie('species'); + + }else if(selectObjId=='species') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get group(cross) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1])) + { + arr[idx++]=lArr[i][1]; + } + } + idx=0; + len = arr.length; + removeOptions("cross"); + for (var i=0; i < len; i++) { + // setting Group's option + groupObj.options[idx++] = new Option(gArr[arr[i]].txt, gArr[arr[i]].val); + } + updateChocie('cross'); + + }else if(selectObjId=='cross') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var typeObj = document.getElementById('tissue'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get type(tissue) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2])) + { + arr[idx++]=lArr[i][2]; + } + } + idx=0; + len = arr.length; + removeOptions("tissue"); + for (var i=0; i < len; i++) { + // setting Type's option + typeObj.options[idx++] = new Option(tArr[arr[i]].txt, tArr[arr[i]].val); + } + updateChocie('tissue'); + + }else if(selectObjId=='tissue') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var typeObj = document.getElementById('tissue'); + var databaseObj = document.getElementById('database'); + + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get dataset(database) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3])) + { + arr[idx++]=lArr[i][3]; + } + } + idx=0; + len = arr.length; + removeOptions("database"); + for (var i=0; i < len; i++) { + // setting Database's option + databaseObj.options[idx++] = new Option(dArr[arr[i]].txt, dArr[arr[i]].val); + } + updateChocie('database'); + } +} + +/* +* input: arr (targeted array); obj (targeted value) +* function: check whether targeted array contains targeted value or not +* output: return true, if array contains targeted value, otherwise return false +*/ +function Contains(arr,obj) { + var i = arr.length; + while (i--) { + if (arr[i] == obj) { + return true; + } + } + return false; +} + +/* +* input: selectObj (designated select menu, such as species, cross, etc... ) +* function: clear designated select menu's option +* output: null +*/ +function removeOptions(selectObj) { + if (typeof selectObj != 'object'){ + selectObj = document.getElementById(selectObj); + } + var len = selectObj.options.length; + for (var i=0; i < len; i++) { + // clear current selection + selectObj.options[0] = null; + } +} + +/* +* input: selectObjId (designated select menu, such as species, cross, etc... ) +* Value: target value +* function: retrieve Index info of target value in designated array +* output: index info +*/ +function getIndexByValue(selectObjId,val) +{ + if(selectObjId=='species') + { + for(var i=1;i<sArr.length;i++){ + if(sArr[i].val==val) + return i; + } + }else if(selectObjId=='cross') + { + for(var i=1;i<gArr.length;i++) + if(gArr[i].val==val) + return i; + }else if(selectObjId=='tissue') + { + for(var i=1;i<tArr.length;i++) + if(tArr[i].val==val) + return i; + } + else return; +} + +/* +* input: objId (designated select menu, such as species, cross, etc... ) +* val(targeted value) +* function: setting option's selected status for designated select menu based on target value, also update the following select menu in the main search page +* output: return true if selected status has been set, otherwise return false. +*/ +function setChoice(objId,val) +{ + var Obj = document.getElementById(objId); + var idx=-1; + + for(i=0;i<Obj.options.length;i++){ + if(Obj.options[i].value==val){ + idx=i; + break; + } + } + + if(idx>=0){ + //setting option's selected status + Obj.options[idx].selected=true; + //update the following select menu + fillOptions(objId); + }else{ + Obj.options[0].selected=true; + fillOptions(objId); + } +} + +// setting option's selected status based on default setting or cookie setting for Species, Group, Type and Database select menu in the main search page http://www.genenetwork.org/ +function updateChocie(selectObjId){ + + if (selectObjId =='species') + { + defaultSpecies= getDefaultValue('species'); + //setting option's selected status + setChoice('species',defaultSpecies); + }else if (selectObjId =='cross') + { + defaultSet= getDefaultValue('cross'); + //setting option's selected status + setChoice('cross',defaultSet); + }else if (selectObjId =='tissue') + { + defaultType= getDefaultValue('tissue'); + //setting option's selected status + setChoice('tissue',defaultType); + }else if (selectObjId =='database') + { + defaultDB= getDefaultValue('database'); + //setting option's selected status + setChoice('database',defaultDB); + } +} + +//get default value;if cookie exists, then use cookie value, otherwise use default value +function getDefaultValue(selectObjId){ + //define default value + var defaultSpecies = 'mouse' + var defaultSet = 'BXD' + var defaultType = 'Hippocampus' + var defaultDB = 'HC_M2_0606_P' + + if (selectObjId =='species') + { + //if cookie exists, then use cookie value, otherwise use default value + var cookieSpecies = getCookie('defaultSpecies'); + if(cookieSpecies) + { + defaultSpecies= cookieSpecies; + } + return defaultSpecies; + }else if (selectObjId =='cross'){ + var cookieSet = getCookie('defaultSet'); + if(cookieSet){ + defaultSet= cookieSet; + } + return defaultSet; + }else if (selectObjId =='tissue'){ + var cookieType = getCookie('defaultType'); + if(cookieType){ + defaultType= cookieType; + } + return defaultType; + }else if (selectObjId =='database') + { + var cookieDB = getCookie('defaultDB'); + if(cookieDB){ + defaultDB= cookieDB; + } + return defaultDB; + } + +} + +//setting default value into cookies for the dropdown menus: Species,Group, Type, and Database +function setDefault(thisform){ + + setCookie('cookieTest', 'cookieTest', 1); + var cookieTest = getCookie('cookieTest'); + delCookie('cookieTest'); + if (cookieTest){ + var defaultSpecies = thisform.species.value; + setCookie('defaultSpecies', defaultSpecies, 10); + var defaultSet = thisform.cross.value; + setCookie('defaultSet', defaultSet, 10); + var defaultType = thisform.tissue.value; + setCookie('defaultType', defaultType, 10); + var defaultDB = thisform.database.value; + setCookie('defaultDB', defaultDB, 10); + updateChocie('species'); + updateChocie('cross'); + updateChocie('tissue'); + updateChocie('database'); + alert("The current settings are now your default"); + } + else{ + alert("You need to enable Cookies in your browser."); + } +} + +''' +# write all strings' info into selectDatasetMenu.js file +fileHandler.write(outputStr) +fileHandler.close() diff --git a/web/webqtl/maintainance/updateMenuJS.py b/web/webqtl/maintainance/updateMenuJS.py new file mode 100755 index 00000000..8b6e25d3 --- /dev/null +++ b/web/webqtl/maintainance/updateMenuJS.py @@ -0,0 +1,127 @@ +# 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 +# +# created by Lei Yan 02/08/2011 +import sys, os +import MySQLdb +import string + + + +abs_path = os.path.abspath(os.path.dirname(__file__)) +path1 = abs_path + "/.." +path2 = abs_path + "/../../javascript" +sys.path.insert(0, path1) + +#must import GN python files after add path +from base import webqtlConfig + +# build MySql database connection +con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD) +cursor = con.cursor() +cursor.execute("SELECT id,menuname FROM Species ORDER BY OrderId") +results = list(cursor.fetchall()) +collectionsText = "" +for result in results: + specieid = result[0] + speciename = result[1] + collectionsText += ("['" + speciename + "', ") + collectionsText += ("null, ") + collectionsText += ("null, ") + collectionsText += "\n" + cursor.execute("select name from InbredSet where speciesid=" + str(specieid)) + results2 = list(cursor.fetchall()) + for result2 in results2: + inbredsetName = result2[0] + if not cmp(inbredsetName, "BXD300"): + continue + collectionsText += "\t" + collectionsText += ("['" + inbredsetName + "', ") + collectionsText += ("'/webqtl/main.py?FormID=dispSelection&RISet=" + inbredsetName + "'], ") + collectionsText += "\n" + collectionsText += "]," + collectionsText += "\n" +collectionsText = collectionsText.strip() + +jstext = """/* + --- menu items --- + note that this structure has changed its format since previous version. + additional third parameter is added for item scope settings. + Now this structure is compatible with Tigra Menu GOLD. + Format description can be found in product documentation. +*/ +var MENU_ITEMS = [ + ['menu_grp1', null, null, + ['GeneNetwork Intro', '/home.html'], + ['Enter Trait Data', '/webqtl/main.py?FormID=submitSingleTrait'], + ['Batch Submission', '/webqtl/main.py?FormID=batSubmit'], + ], + ['menu_grp2', null, null, + ['Search Databases', '/'], + ['Tissue Correlation', '/webqtl/main.py?FormID=tissueCorrelation'], + ['SNP Browser', '/webqtl/main.py?FormID=snpBrowser'], + ['Gene Wiki', '/webqtl/main.py?FormID=geneWiki'], + ['Interval Analyst', '/webqtl/main.py?FormID=intervalAnalyst'], + ['QTLminer', '/webqtl/main.py?FormID=qtlminer'], + ['GenomeGraph', '/dbResults.html'], + ['Trait Collections',null,null, +%s + ], + ['Scriptable Interface', '/CGIDoc.html'], + /* ['Simple Query Interface', '/GUI.html'], */ + ['Database Information',null,null, + ['Database Schema', '/webqtl/main.py?FormID=schemaShowPage'], + ], + ['Data Sharing', '/webqtl/main.py?FormID=sharing'], + ['Microarray Annotations', '/webqtl/main.py?FormID=annotation'], + ], + ['menu_grp3', null, null, + ['Movies','http://www.genenetwork.org/tutorial/movies'], + ['Tutorials', null, null, + ['GN Barley Tutorial','/tutorial/pdf/GN_Barley_Tutorial.pdf'], + ['GN Powerpoint', '/tutorial/ppt/index.html']], + ['HTML Tour','/tutorial/WebQTLTour/'], + ['FAQ','/faq.html'], + ['Glossary of Terms','/glossary.html'], + ['GN MediaWiki','http://wiki.genenetwork.org/'], + ], + ['menu_grp4', '/whats_new.html' + ], + ['menu_grp5', '/reference.html' + ], + ['menu_grp6', null, null, + ['Conditions and Limitation', '/conditionsofUse.html'], + ['Data Sharing Policy', '/dataSharing.html'], + ['Status and Contacts', '/statusandContact.html'], + ['Privacy Policy', '/privacy.html'], + ], + ['menu_grp8', '/links.html' + ], +]; +""" + +# create menu_items.js file +fileHandler = open(path2 + '/menu_items.js', 'w') +fileHandler.write(jstext % collectionsText) +fileHandler.close() |