diff options
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 724 |
1 files changed, 119 insertions, 605 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 7d2605c1..33813051 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -19,622 +19,136 @@ # # # 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 . +# This script is to generate the data for the main menus on the home page +# It needs to be run manually when database has been changed . from __future__ import print_function, division -import sys, os +import sys -current_file_name = __file__ -pathname = os.path.dirname( current_file_name ) -abs_path = os.path.abspath(pathname) -sys.path.insert(0, abs_path + '/..') +sys.path.insert(0, "..") 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') +import simplejson as json -# 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' +from pprint import pformat as pf -# 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 +from base import webqtlConfig - 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" +# 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() + + +def get_species(): + """Build species list""" + Cursor.execute("select Name, MenuName from Species order by OrderId") + species = list(Cursor.fetchall()) + return species + + +def get_groups(species): + """Build groups list""" + groups = {} + for species_name, _species_full_name in species: + Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet, + Species, + ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s + and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and + (PublishFreeze.InbredSetId = InbredSet.Id + or GenoFreeze.InbredSetId = InbredSet.Id + or ProbeFreeze.InbredSetId = InbredSet.Id) + group by InbredSet.Name + order by InbredSet.Name""", (species_name)) + groups[species_name] = list(Cursor.fetchall()) + return groups + + +def get_types(groups): + """Build types list""" + types = {} + for species, group_dict in groups.iteritems(): + types[species] = {} + for group_name, _group_full_name in group_dict: + # make group an alias to shorten the code + group = types[species][group_name] = [("Phenotypes", "Phenotypes"), + ("Genotypes", "Genotypes")] + 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 = %s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.public > %s + order by Tissue.Name""", (group_name, webqtlConfig.PUBLICTHRESH)) + group += Cursor.fetchall() + return types + + +def get_datasets(types): + """Build datasets list""" + datasets = {} + for species, group_dict in types.iteritems(): + datasets[species] = {} + for group, type_list in group_dict.iteritems(): + datasets[species][group] = {} + for type_name, type_full_name in type_list: + dataset_text = dataset_value = None + if type_name == "Phenotypes": + dataset_value = "%sPublish" % group + if group == 'MDP': + dataset_text = "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" + dataset_text = "%s Published Phenotypes" % group + + elif type_name == "Genotypes": + dataset_value = "%sGeno" % group + dataset_text = "%s Genotypes" % group + + if dataset_value: + datasets[species][group][type_name] = [(dataset_value, dataset_text)] 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() + Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from + ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s + and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = + InbredSet.Id and ProbeSetFreeze.public > %s order by + ProbeSetFreeze.CreateTime desc""", (type_name, + webqtlConfig.PUBLICTHRESH)) + datasets[species][group][type_name] = Cursor.fetchall() + + return datasets + + +def main(): + species = get_species() + groups = get_groups(species) + types = get_types(groups) + datasets = get_datasets(types) + + species.append(('All Species', 'All Species')) + groups['All Species'] = [('All Groups', 'All Groups')] + types['All Species'] = {} + types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')] + datasets['All Species'] = {} + datasets['All Species']['All Groups'] = {} + datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')] + + data = dict(species=species, + groups=groups, + types=types, + datasets=datasets, + ) + + output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" + + with open(output_file, 'w') as fh: + json.dump(data, fh, indent=" ", sort_keys=True) + + +if __name__ == '__main__': + main()
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