Created header and set defaults for the search dropdown options

3 files changed, 42 insertions, 419 deletions

diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
index a58efe2e..16590e26 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
@@ -24,7 +24,7 @@ $ ->
         redo_dropdown($('#group'), group_list)
         populate_type()
     window.populate_group = populate_group
-        
+
     populate_type = ->
         species = $('#species').val()
         group = $('#group').val()
@@ -32,7 +32,7 @@ $ ->
         redo_dropdown($('#type'), type_list)
         populate_dataset()
     window.populate_type = populate_type
-        
+
     populate_dataset = ->
         species = $('#species').val()
         group = $('#group').val()
@@ -59,11 +59,13 @@ $ ->
         populate_dataset()
 
     ## Info buttons
-    
+
     open_window = (url, name) ->
         options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900"
         open(url, name, options).focus()
 
+    # Link to info on selected group; use of "Cross"
+    # in the url is outdated and should be changed to group
     group_info = ->
         species = $('#species').val()
         group = $('#group').val()
@@ -72,6 +74,7 @@ $ ->
 
     $('#group_info').click(group_info)
 
+    # Link to dataset info
     dataset_info = ->
         dataset = $('#dataset').val()
         url = "/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset
@@ -81,7 +84,7 @@ $ ->
 
 
     ## Handle setting new default drop downs
-    
+
     make_default = ->
         holder = {}
         for item in ['species', 'group', 'type', 'dataset']
@@ -89,425 +92,31 @@ $ ->
         jholder = JSON.stringify(holder)
         $.cookie('search_defaults', jholder,
                  expires: 365)
-        
+
     apply_default = ->
         defaults = $.cookie('search_defaults')
-        if not defaults
-            return
-        defaults = $.parseJSON(defaults)
-        
+        if defaults
+            # defaults are stored as a JSON string in a cookie
+            defaults = $.parseJSON(defaults)
+        else
+            # If user hasn't set a default we use this
+            # (Most of GN's data is from BXD mice)
+            defaults =
+                species: "mouse"
+                group: "BXD"
+                type: "Hippocampus"
+                dataset: "HC_M2_0606_P"
+
         for item in [['species', 'group']
                      ['group', 'type']
                      ['type', 'dataset'],
                      ['dataset', null]]
-    
             $("##{item[0]}").val(defaults[item[0]])
+
             if item[1]
                 populate_function = "populate_" + item[1]
                 console.log("Calling:", populate_function)
                 window[populate_function]()
-    
-        
-        
-    $("#make_default").click(make_default)
-    
 
-## 
-##*  function: based on different browser use, will have different initial actions; 
-##*  Once the index.html page is loaded, this function will be called
-##
-#
-#$ ->
-#    
-#    fillSpecies = ->
-#        
-#    
-#    
-#    
-#    sArr =window.sArr   # species
-#    gArr = window.gArr   # group
-#    tArr = window.tArr
-#    dArr = window.dArr
-#    lArr = window.lArr
-#    
-#    console.log("sArr is now [jersey]:", sArr)
-#    console.log("gArr is now [jersey]:", gArr)
-#    
-#    initialDatasetSelection = ->
-#        defaultSpecies = getDefaultValue("species")
-#        defaultSet = getDefaultValue("cross")
-#        defaultType = getDefaultValue("tissue")
-#        defaultDB = getDefaultValue("database")
-#        if navigator.userAgent.indexOf("MSIE") >= 0
-#            sOptions = fillOptionsForIE(null, defaultSpecies)
-#            menu0 = "<SELECT NAME='species' ID='species' SIZE='1' onChange='fillOptions(\"species\");'>" + sOptions + "</Select>"
-#            document.getElementById("menu0").innerHTML = menu0
-#            gOptions = fillOptionsForIE("species", defaultSet)
-#            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)
-#            menu2 = "<Select NAME='tissue' size=1 id='tissue' onchange='fillOptions(\"tissue\");'>" + tOptions + "</Select>"
-#            document.getElementById("menu2").innerHTML = menu2
-#            dOptions = fillOptionsForIE("tissue", defaultDB)
-#            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
-#    #
-#    fillOptionsForIE = (selectObjId, defaultValue) ->
-#        options = ""
-#        unless selectObjId?
-#            len = sArr.length
-#            i = 1
-#    
-#            while i < len
-#                
-#                # setting Species' option			
-#                if sArr[i].val is 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>"
-#                i++
-#        else if selectObjId is "species"
-#            speciesObj = document.getElementById("species")
-#            len = lArr.length
-#            arr = []
-#            idx = 0
-#            i = 1
-#    
-#            while i < len
-#                
-#                #get group(cross) info from lArr
-#                arr[idx++] = lArr[i][1]  if lArr[i][0] is (getIndexByValue("species", speciesObj.value)).toString() and not Contains(arr, lArr[i][1])
-#                i++
-#            idx = 0
-#            len = arr.length
-#            removeOptions "cross"
-#            i = 0
-#    
-#            while i < len
-#                
-#                # setting Group's option
-#                if gArr[arr[i]].val is 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>"
-#                i++
-#        else if selectObjId is "cross"
-#            speciesObj = document.getElementById("species")
-#            groupObj = document.getElementById("cross")
-#            len = lArr.length
-#            arr = []
-#            idx = 0
-#            i = 1
-#    
-#            while i < len
-#                
-#                #get type(tissue) info from lArr
-#                arr[idx++] = lArr[i][2]  if lArr[i][0] is (getIndexByValue("species", speciesObj.value)).toString() and lArr[i][1] is (getIndexByValue("cross", groupObj.value)).toString() and not Contains(arr, lArr[i][2])
-#                i++
-#            idx = 0
-#            len = arr.length
-#            removeOptions "tissue"
-#            i = 0
-#    
-#            while i < len
-#                
-#                # setting Type's option
-#                if tArr[arr[i]].val is 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>"
-#                i++
-#        else if selectObjId is "tissue"
-#            speciesObj = document.getElementById("species")
-#            groupObj = document.getElementById("cross")
-#            typeObj = document.getElementById("tissue")
-#            len = lArr.length
-#            arr = []
-#            idx = 0
-#            i = 1
-#    
-#            while i < len
-#                
-#                #get dataset(database) info from lArr
-#                arr[idx++] = lArr[i][3]  if lArr[i][0] is (getIndexByValue("species", speciesObj.value)).toString() and lArr[i][1] is (getIndexByValue("cross", groupObj.value)).toString() and lArr[i][2] is (getIndexByValue("tissue", typeObj.value)).toString() and not Contains(arr, lArr[i][3])
-#                i++
-#            idx = 0
-#            len = arr.length
-#            removeOptions "database"
-#            i = 0
-#    
-#            while i < len
-#                
-#                # setting Database's option			
-#                if dArr[arr[i]].val is 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>"
-#                i++
-#        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
-#    #
-#    fillOptions = (selectObjId) ->
-#        console.log("[vacuum] selectObjId:", selectObjId)
-#        unless selectObjId?
-#            speciesObj = document.getElementById("species")
-#            console.log("speciesObj:", speciesObj)
-#            len = sArr.length
-#            i = 1
-#    
-#            while i < len
-#                
-#                # setting Species' option
-#                speciesObj.options[i - 1] = new Option(sArr[i].txt, sArr[i].val)
-#                console.log("speciesObj.options:", speciesObj.options[i - 1])
-#                i++
-#            updateChoice "species"
-#        else if selectObjId is "species"
-#            speciesObj = document.getElementById("species")
-#            console.log("speciesObj:", speciesObj)
-#            groupObj = document.getElementById("cross")
-#            console.log("groupObj:", groupObj)
-#            len = lArr.length
-#            arr = []
-#            idx = 0
-#            i = 1
-#
-#            while i < len
-#                #get group(cross) info from lArr
-#                index_value = getIndexByValue("species", speciesObj.value).toString()
-#                if lArr[i][0] is (index_value and not Contains(arr, lArr[i][1]))
-#                    arr[idx++] = lArr[i][1] 
-#                i++
-#            idx = 0
-#            len = arr.length
-#            removeOptions "cross"
-#            i = 0
-#    
-#            while i < len
-#                # setting Group's option
-#                groupObj.options[idx++] = new Option(gArr[arr[i]].txt, gArr[arr[i]].val)
-#                i++
-#            updateChoice "cross"
-#        else if selectObjId is "cross"
-#            speciesObj = document.getElementById("species")
-#            groupObj = document.getElementById("cross")
-#            typeObj = document.getElementById("tissue")
-#            len = lArr.length
-#            arr = []
-#            idx = 0
-#            i = 1
-#    
-#            while i < len
-#                
-#                #get type(tissue) info from lArr
-#                arr[idx++] = lArr[i][2]  if lArr[i][0] is (getIndexByValue("species", speciesObj.value)).toString() and lArr[i][1] is (getIndexByValue("cross", groupObj.value)).toString() and not Contains(arr, lArr[i][2])
-#                i++
-#            idx = 0
-#            len = arr.length
-#            removeOptions "tissue"
-#            i = 0
-#    
-#            while i < len
-#                
-#                # setting Type's option
-#                typeObj.options[idx++] = new Option(tArr[arr[i]].txt, tArr[arr[i]].val)
-#                i++
-#            updateChoice "tissue"
-#        else if selectObjId is "tissue"
-#            speciesObj = document.getElementById("species")
-#            groupObj = document.getElementById("cross")
-#            typeObj = document.getElementById("tissue")
-#            databaseObj = document.getElementById("database")
-#            len = lArr.length
-#            arr = []
-#            idx = 0
-#            i = 1
-#    
-#            while i < len
-#                
-#                #get dataset(database) info from lArr
-#                arr[idx++] = lArr[i][3]  if lArr[i][0] is (getIndexByValue("species", speciesObj.value)).toString() and lArr[i][1] is (getIndexByValue("cross", groupObj.value)).toString() and lArr[i][2] is (getIndexByValue("tissue", typeObj.value)).toString() and not Contains(arr, lArr[i][3])
-#                i++
-#            idx = 0
-#            len = arr.length
-#            removeOptions "database"
-#            i = 0
-#    
-#            while i < len
-#                
-#                # setting Database's option
-#                databaseObj.options[idx++] = new Option(dArr[arr[i]].txt, dArr[arr[i]].val)
-#                i++
-#            updateChoice "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
-#    #
-#    Contains = (arr, obj) ->
-#        i = arr.length
-#        return true  if arr[i] is obj  while i--
-#        false
-#    
-#    # 
-#    #* input: selectObj (designated select menu, such as species, cross, etc... )
-#    #* function: clear designated select menu's option
-#    #* output: null
-#    #
-#    removeOptions = (selectObj) ->
-#        selectObj = document.getElementById(selectObj)  unless typeof selectObj is "object"
-#        len = selectObj.options.length
-#        i = 0
-#    
-#        while i < len
-#            
-#            # clear current selection       
-#            selectObj.options[0] = null
-#            i++
-#    
-#    # 
-#    #*  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
-#    #
-#    getIndexByValue = (selectObjId, val) ->
-#        if selectObjId is "species"
-#            i = 1
-#    
-#            while i < sArr.length
-#                return i  if sArr[i].val is val
-#                i++
-#        else if selectObjId is "cross"
-#            i = 1
-#    
-#            while i < gArr.length
-#                return i  if gArr[i].val is val
-#                i++
-#        else if selectObjId is "tissue"
-#            i = 1
-#    
-#            while i < tArr.length
-#                return i  if tArr[i].val is val
-#                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.
-#    #
-#    setChoice = (objId, val) ->
-#        console.log("objId:", objId)
-#        console.log("val:", val)
-#        Obj = document.getElementById(objId)
-#        console.log("Obj:", Obj)
-#        idx = -1
-#        i = 0
-#        while i < Obj.options.length
-#            if Obj.options[i].value is val
-#                idx = i
-#                break
-#            i++
-#        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/
-#    updateChoice = (selectObjId) ->
-#        if selectObjId is "species"
-#            defaultSpecies = getDefaultValue("species")
-#            
-#            #setting option's selected status
-#            setChoice "species", defaultSpecies
-#        else if selectObjId is "cross"
-#            defaultSet = getDefaultValue("cross")
-#            
-#            #setting option's selected status
-#            setChoice "cross", defaultSet
-#        else if selectObjId is "tissue"
-#            defaultType = getDefaultValue("tissue")
-#            
-#            #setting option's selected status
-#            setChoice "tissue", defaultType
-#        else if selectObjId is "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
-#    getDefaultValue = (selectObjId) ->
-#        
-#        #define default value
-#        defaultSpecies = "mouse"
-#        defaultSet = "BXD"
-#        defaultType = "Hippocampus"
-#        defaultDB = "HC_M2_0606_P"
-#        if selectObjId is "species"
-#            
-#            #if cookie exists, then use cookie value, otherwise use default value
-#            cookieSpecies = getCookie("defaultSpecies")
-#            defaultSpecies = cookieSpecies  if cookieSpecies
-#            defaultSpecies
-#        else if selectObjId is "cross"
-#            cookieSet = getCookie("defaultSet")
-#            defaultSet = cookieSet  if cookieSet
-#            defaultSet
-#        else if selectObjId is "tissue"
-#            cookieType = getCookie("defaultType")
-#            defaultType = cookieType  if cookieType
-#            defaultType
-#        else if selectObjId is "database"
-#            cookieDB = getCookie("defaultDB")
-#            defaultDB = cookieDB  if cookieDB
-#            defaultDB
-#    
-#    #setting default value into cookies for the dropdown menus: Species,Group, Type, and Database 
-#    setDefault = (thisform) ->
-#        setCookie "cookieTest", "cookieTest", 1
-#        cookieTest = getCookie("cookieTest")
-#        delCookie "cookieTest"
-#        if cookieTest
-#            defaultSpecies = thisform.species.value
-#            setCookie "defaultSpecies", defaultSpecies, 10
-#            defaultSet = thisform.cross.value
-#            setCookie "defaultSet", defaultSet, 10
-#            defaultType = thisform.tissue.value
-#            setCookie "defaultType", defaultType, 10
-#            defaultDB = thisform.database.value
-#            setCookie "defaultDB", defaultDB, 10
-#            updateChoice "species"
-#            updateChoice "cross"
-#            updateChoice "tissue"
-#            updateChoice "database"
-#            alert "The current settings are now your default"
-#        else
-#            alert "You need to enable Cookies in your browser."
-#            
-#    # run it
-#    initialDatasetSelection()
\ No newline at end of file
+
+    $("#make_default").click(make_default)
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
index 681e4301..5e19ca46 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
@@ -105,10 +105,16 @@
     apply_default = function() {
       var defaults, item, populate_function, _i, _len, _ref, _results;
       defaults = $.cookie('search_defaults');
-      if (!defaults) {
-        return;
+      if (defaults) {
+        defaults = $.parseJSON(defaults);
+      } else {
+        defaults = {
+          species: "mouse",
+          group: "BXD",
+          type: "Hippocampus",
+          dataset: "HC_M2_0606_P"
+        };
       }
-      defaults = $.parseJSON(defaults);
       _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
       _results = [];
       for (_i = 0, _len = _ref.length; _i < _len; _i++) {
diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html
index 51d963fc..695129a9 100644
--- a/wqflask/wqflask/templates/new_index_page.html
+++ b/wqflask/wqflask/templates/new_index_page.html
@@ -35,8 +35,16 @@
               <li class="active">
                 <a href="/">Home</a>
               </li>
-              <li class="">
-                <a href="#">Search</a>
+              <li class="dropdown">
+                <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
+                    Search <b class="caret"></b>
+                </a>
+                    <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
+                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
+                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
+                        <li class="divider"></li>
+                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
+                    </ul>
               </li>
               <li class="">
                 <a href="#">Help</a>