rbbt-rest 1.7.19 → 1.7.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a370ffece6117d1fb32747e5701e9f46858be458
-  data.tar.gz: 4ea778ce9a36602c8346ba96bf3dc62f07a47066
+  metadata.gz: a40ff490d992383fabd6576ad3b06df0c1a9e7c4
+  data.tar.gz: d6ea9091bd3dca0e92f0628ef84b477a6e43f344
 SHA512:
-  metadata.gz: a72b386310566ea2aac5a86dda0a8d89f00b08d11f8066edbdaa99178972a23bd7f0749edf1d10825e53297a1397d499d78d1fefb6d91ac32ce572edb7b4402f
-  data.tar.gz: 43d2059b419238e5bb05737494806f175ace47735f271f039607acfe43ba73a18c49324fc2b78f453fdb072a563fb13cade7d45047e21ef0c922aa708952414e
+  metadata.gz: 5b813d5e2dfe4bbd36b1676a569393f7903eb8f1eb14c9392ed583991fa22cbdfea40b63f910642c5cce50610040154925aa23987855ed7c0112d15b2881754c
+  data.tar.gz: b70426b8a0d31ce739e551c23ca91ab6823aa2bc9b6036f31cf988b6327fd33bb15577ae6aef3c1c740288d46ba7139b53506df9cdb9eaad8ce8557c651aa03c

data/lib/rbbt/rest/common/cache.rb

@@ -58,9 +58,21 @@ module RbbtRESTHelpers
     clean_url = remove_GET_param(clean_url, :_update)
     clean_url = remove_GET_param(clean_url, :_)
 
-    class << step; def url; @url; end; end
+    class << step
+      def url
+        @url
+      end
+
+      def knowledge_base(organism = Organism.default_code("Hsa"))
+        @_kb ||= begin
+                   kb_dir = self.file('knowledge_base')
+                   KnowledgeBase.new kb_dir, organism
+                 end
+      end
+    end
     step.instance_variable_set(:@url, clean_url)
 
+    Thread.current["step_path"] = step.path
     # Issue
     if not step.started?
       if cache_type == :synchronous or cache_type == :sync

data/lib/rbbt/rest/common/misc.rb

@@ -264,12 +264,14 @@ module Haml::Filters::DeferJS
   include Haml::Filters::Base
 
   def render(text)
+    step_path = Thread.current["step_path"]
     defer_text =<<-EOF
 %script
   :plain
-    defer(function(){
+    defer(function(step_path){
+
 #{text.gsub(/^/,"      ")}
-    })
+    }, '#{step_path}')
 EOF
     Haml::Engine.new(defer_text).to_html 
   end

data/lib/rbbt/rest/common/users.rb

@@ -69,6 +69,11 @@ module Sinatra
           redirect '/login'
         end
       end
+      
+      app.get '/logout' do
+        session[:user] = nil
+        redirect '/'
+      end
     end
   end
 

data/lib/rbbt/rest/entity.rb

@@ -542,7 +542,8 @@ module Sinatra
           begin
             res = list.send(property,*args)
           rescue
-            if list.respond_to?(:format) and  list.base_type.respond_to?(:default_format) and list.format != list.base_type.default_format
+            Log.exception $!
+            if list.respond_to?(:format) and list.base_type.respond_to?(:default_format) and list.format != list.base_type.default_format
               list = list.to(:default)
               Log.warn "Error computing property #{property} for list. Automatically changing list format to default"
               retry

data/lib/rbbt/rest/knowledge_base.rb

@@ -309,8 +309,9 @@ module Sinatra
           source_type = kb.source_type(database)
           target_type = kb.target_type(database)
           fields = kb.fields(database)
-          source_entity_options = kb.entity_options_for source_type
-          target_entity_options = kb.entity_options_for target_type
+          source_entity_options = kb.entity_options_for source_type, database
+          target_entity_options = kb.entity_options_for target_type, database
+          undirected = kb.undirected(database) == 'undirected'
 
           info = {
             :source => source,
@@ -320,6 +321,7 @@ module Sinatra
             :source_entity_options => source_entity_options,
             :target_entity_options => target_entity_options,
             :fields => fields,
+            :undirected => undirected,
           }
 
           halt 200, info.to_json
@@ -539,6 +541,7 @@ module Sinatra
           content_type "application/json"
           halt 200, serialize_entities(list).to_json
         end
+
       end
     end
   end

data/lib/rbbt/rest/knowledge_base/helpers.rb

@@ -53,6 +53,10 @@ module KnowledgeBaseRESTHelpers
 
   def get_knowledge_base(name=:user, namespace = nil)
     kb = case name.to_s
+           when 'step'
+             dir = cookies[:step_path] + '.files/knowledge_base'
+             iii dir
+             KnowledgeBase.load(dir)
            when "user"
              user_kb(user)
            else
@@ -90,4 +94,9 @@ module KnowledgeBaseRESTHelpers
       {:id => e, :name => name, :type => e.base_type, :info => e.info}
     end
   end
+
+  def get_matrix(code)
+    name, study = code.split("@")
+    Study.setup(study).matrix(name)
+  end
 end

data/lib/rbbt/rest/main.rb

@@ -7,6 +7,7 @@ require 'ruby-prof'
 require 'sinatra/base'
 require 'sinatra/cross_origin'
 require "sinatra/multi_route"
+require "sinatra/cookies"
 require 'json'
 
 module Sinatra
@@ -41,6 +42,7 @@ module Sinatra
 
         helpers RbbtRESTHelpers
         register Sinatra::RbbtAuth
+        helpers Sinatra::Cookies
 
         add_sass_load_path Rbbt.share.views.compass.find(:lib)
 

data/share/views/compass/app.sass

@@ -41,3 +41,9 @@ a.entity
       float: right
       height: 22px
 
+.content > .info
+  &:hover
+    z-index: 10
+
+table > caption
+  max-width: 60em

data/share/views/layout/header.haml

@@ -30,9 +30,12 @@
   requirejs.config({baseUrl: '/js-find'})
 
 
+-# Cookies
+- record_js '/plugins/js-cookie/js/js.cookie.js'
 
 -# JQUERY JS
-- %w(jquery-2.1.1 jquery.cookie jquery.form).each do |jquery_file|
+-# %w(jquery-2.1.1 jquery.cookie jquery.form).each do |jquery_file|
+- %w(jquery-2.1.1 jquery.form).each do |jquery_file|
   - record_js File.join('/plugins/jquery/js/', jquery_file)
 
 - record_js '/plugins/jquery-ui/js/jquery-ui-1.8.14.custom.min.js'
@@ -53,8 +56,6 @@
 - record_js '/plugins/cola/js/cola.js'
 - record_js '/plugins/mithril-node-render/js/index.js'
 
-
-
 - %w(helpers _md5 _ajax_replace _ellipsis).each do |file|
   - record_js "/js-find/helpers/#{ file }"
 
@@ -65,7 +66,10 @@
 - %w(rbbt rbbt.basic rbbt.exception rbbt.job rbbt.page rbbt.entity.basic rbbt.entity rbbt.entity_list rbbt.entity_map rbbt.views rbbt.favourites rbbt.modal).each do |file|
   - record_js "/js-find/#{ file }"
 
-- %w(rbbt.knowledge_base rbbt.aesthetics rbbt.plots rbbt.aes_plots).each do |file|
+- %w(rbbt.knowledge_base).each do |file|
   - record_js "/js-find/#{ file }"
 
+- %w(rbbt.plots.basic rbbt.plots.aes rbbt.plots.graph rbbt.plots.graph.kb rbbt.plots.graph.adapters rbbt.plots.aesthetics rbbt.plots.list).each do |file|
+  - record_js "/js-find/rbbt.plots/#{ file }"
+
 - record_js "/js-find/app"

data/share/views/public/js/helpers/defer.js

@@ -1,25 +1,27 @@
 var deferred_execution = [];
 
-function defer(deps, func){
+function defer(deps, func, step_path){
+  if (typeof func == 'string'){
+    step_path = func
+    func = deps
+    deps = undefined;
+  }
   if (undefined === func){
     func = deps;
     deps = undefined;
   }
-  if (undefined !== deps){
-    deferred_execution.push([deps, func]);
-  }else{
-    deferred_execution.push(func)
-  }
+  document.step_path = step_path
+  deferred_execution.push([func, deps, step_path]);
 }
 
 function start_deferred(){
   var tmp = $.unique(deferred_execution);
   deferred_execution = [];
   $(tmp).each(function(pos,func){
-    if (typeof(func) == 'object'){
-      require_js(func[0], func[1]);
+    if (undefined === func[1]){
+      rbbt.try(func[0])(func[2])
     }else{
-      rbbt.try(func).call()
+      require_js(func[1], func[0], func[2]);
     }
   })
   return(false)

data/share/views/public/js/helpers/helpers.js

@@ -57,7 +57,7 @@ function parse_parameters(params){
 }
 
 var required_js = [];
-function require_js(url, success){
+function require_js(url, success, script){
  if (typeof url == 'object'){
    if (url.length > 1){
     var u = url.shift()
@@ -82,9 +82,9 @@ function require_js(url, success){
   url = url.replace('/js/', '/js-find/')
 
   if ($.inArray(url, required_js) >= 0){
-    if (typeof success == 'function'){ success.call() }
+    if (typeof success == 'function'){ success.call(script) }
   }else{
-    var _success = function(){ required_js.push(url); if (typeof success == 'function'){ success.call() }; }
+    var _success = function(){ required_js.push(url); if (typeof success == 'function'){ success.call(script) }; }
     $.ajax({url: url, cache:cache, dataType:'script', async: async, success: _success} ).fail(function(jqxhr, settings, exception){ console.log('Failed to load ' + url) })
   }
  }
@@ -105,6 +105,16 @@ function merge_hash(destination, source){
   return destination;
 }
 
+function clean_hash(h){
+  var clean = {}
+
+  forHash(h, function(k,v){
+    if (undefined !== v) clean[k] = v
+  })
+
+  return clean
+}
+
 function array_values(hash){
   var tmp_arr = [], key = '';
   for (key in hash) {
@@ -195,12 +205,16 @@ function get_gradient(values, color1, color2){
   var color2 = Color(color2)
   var steps = values.length
   var clean_values = []
-  forArray(values,function(v){ if (typeof v == 'number' && ! isNaN(v)) clean_values.push(v) })
+  forArray(values,function(v){ 
+    if (typeof v == 'string') v = parseFloat(v)
+    if (typeof v == 'number' && ! isNaN(v)) clean_values.push(v) 
+  })
   var max = Math.max.apply(null,clean_values)
   var min = Math.min.apply(null,clean_values)
   var diff = max - min
   var colors = []
   forArray(values, function(value){
+    if (typeof value == 'string') value = parseFloat(value)
     if (typeof value == 'number'){
       var a = (value - min)/diff
       colors.push(color1.blend(color2, a).toString())
@@ -218,11 +232,15 @@ function get_sign_gradient(values, color1, color0, color2){
   var color2 = Color(color2)
   var steps = values.length
   var clean_values = []
-  forArray(values,function(v){ if (typeof v == 'number' && ! isNaN(v)) clean_values.push(v) })
+  forArray(values,function(v){ 
+    if (typeof v == 'string') v = parseFloat(v)
+    if (typeof v == 'number' && ! isNaN(v)) clean_values.push(v) 
+  })
   var max = Math.max.apply(null,clean_values)
   var min = Math.min.apply(null,clean_values)
   var colors = []
   forArray(values, function(value){
+    if (typeof value == 'string') value = parseFloat(value)
     if (typeof value == 'number'){
       if (value > 0){
         var a = value/max

data/share/views/public/js/rbbt.basic.js

@@ -11,7 +11,21 @@ rbbt.ajax = function(params){
   }else{
     params.config = function(xhr, options){ xhr.setRequestHeader( "X-Requested-With", "XMLHttpRequest"); return xhr; }
   }
-  return m.request(params)
+
+  if (params.cookies){
+    forHash(params.cookies, function(k,v){rbbt.set_cookie(k,v)})
+    params.cookies_set = true
+    params.onreadystatechange = function(){
+      if (params.cookies_set){
+        forHash(params.cookies, function(k,v){rbbt.remove_cookie(k)})
+        params.cookies_set = false
+      }
+    }
+  }
+
+  req = m.request(params)
+
+  return req
 }
 
 rbbt.insist_request = function(params, deferred, timeout, missing){
@@ -54,6 +68,7 @@ rbbt.post = function(url, data, params){
     if (undefined === params.url) params.url = url
 
     request_params = {url: url, method: "POST", data: data, serialize: function(formData){return formData} }
+    forHash(params, function(k,v){request_params[k] = v})
   }
 
   if (undefined === request_params.method) request_params.method = 'POST'
@@ -74,6 +89,22 @@ rbbt.post = function(url, data, params){
   return rbbt.insist_request(request_params)
 }
 
+// Cookies
+
+rbbt.set_cookie = function(name,value){
+  Cookies.set(name, value)
+}
+
+rbbt.get_cookie = function(name){
+  if (undefined === name)
+    return Cookies.get()
+  else
+    return Cookies.get(name)
+}
+
+rbbt.remove_cookie = function(name){
+  Cookies.remove(name)
+}
 
 // LocalStorage
 

data/share/views/public/js/rbbt.entity.basic.js

@@ -38,21 +38,37 @@ rbbt.entity_array.property = function(codes, type, info, name, args){
   return rbbt.post(url, data)
 }
 
-rbbt.entity_array.parents = function(codes, type, database){
-   var url = '/knowledge_base/user/' + database + '/collection_parents' 
-   
-   var collection = {}
-   collection[type] = codes
-   
-   var data = {}
-   data.collection = collection
-   data._format = 'tsv_json'
-   
-   return rbbt.post(url, data)
+rbbt.entity_array.parents = function(codes, type, database_code){
+  var parts = rbbt.knowledge_base.parse_db(database_code)
+  var kb,database,params
+  kb = parts[0]; database = parts[1], cookies = parts[2]
+
+  var params = {}
+
+  params.cookies = cookies
+
+  var url = '/knowledge_base/'+kb+'/' + database + '/collection_parents' 
+
+  var collection = {}
+  collection[type] = codes
+
+  var data = {}
+  data.collection = collection
+  data._format = 'tsv_json'
+
+  return rbbt.post(url, data,params)
 }
 
-rbbt.entity_array.children = function(codes, type, database){
-   var url = '/knowledge_base/user/' + database + '/collection_parents' 
+rbbt.entity_array.children = function(codes, type, database_code){
+  var parts = rbbt.knowledge_base.parse_db(database_code)
+  var kb,database,params
+  kb = parts[0]; database = parts[1], cookies = parts[2]
+
+   var params = {}
+
+   params.cookies = cookies
+
+   var url = '/knowledge_base/'+kb+'/' + database + '/collection_children' 
    
    var collection = {}
    collection[type] = codes
@@ -61,11 +77,19 @@ rbbt.entity_array.children = function(codes, type, database){
    data.collection = collection
    data._format = 'tsv_json'
    
-   return rbbt.post(url, data)
+   return rbbt.post(url, data,params)
 }
 
-rbbt.entity_array.subset = function(database, source, target){
-   var url = '/knowledge_base/user/' + database + '/subset' 
+rbbt.entity_array.subset = function(database_code, source, target){
+  var parts = rbbt.knowledge_base.parse_db(database_code)
+  var kb,database,params
+  kb = parts[0]; database = parts[1], cookies = parts[2]
+
+   var params = {}
+
+   params.cookies = cookies
+
+   var url = '/knowledge_base/' + kb + '/' + database + '/subset' 
 
    var data = {}
    var source = source.join(",")
@@ -73,5 +97,5 @@ rbbt.entity_array.subset = function(database, source, target){
    data.source = source
    if (target) data.target = target.join(",")
 
-   return rbbt.post(url, data)
+   return rbbt.post(url, data, params)
 }

data/share/views/public/js/rbbt.knowledge_base.js

@@ -14,21 +14,72 @@ var KB = rbbt.knowledge_base = {}
 // return m.request({url: url, method: "GET", type: Entity})
 //}
 
-KB.database_info = function(database){
- var url = '/knowledge_base/user/' + database + '/info'
- url = add_parameter(url, '_format', 'json')
- return m.request({url: url, method: "GET"})
+rbbt.step_path = function(path, func){
+  if (undefined === path){
+    if (typeof step_path == 'string')
+      return step_path
+    if (rbbt._step_path)
+      return rbbt._step_path
+    else{
+      if (document.step_path)
+        return document.step_path
+      else
+        return undefined
+    }
+  }else{
+    old = rbbt._step_path
+    rbbt._step_path = path
+  }
+
+  if (undefined === func)
+    return
+  else{
+    func()
+    rbbt._step_path = old
+  }
+}
+
+KB.parse_db = function(database_code){
+   var kb = 'user'
+   var database
+
+   if (database_code.indexOf(':') > 0){
+     var parts = database_code.split(":")
+     kb = parts[0]
+     database = parts[1]
+   }else{
+     database = database_code
+   }
+
+   if (kb == 'step'){
+     var path
+     if (typeof step_path != 'undefined') path = step_path
+     if (undefined === path) path = rbbt.step_path()
+     cookies = {step_path: path}
+   }else
+     cookies = undefined
+
+   return [kb, database, cookies]
+}
+
+KB.database_info = function(database_code){
+  var parts = rbbt.knowledge_base.parse_db(database_code)
+  var kb,database,params
+  kb = parts[0]; database = parts[1], cookies = parts[2]
+
+  var url = '/knowledge_base/' + kb + '/' + database + '/info' 
+
+  url = add_parameter(url, '_format', 'json')
+
+  params = {url: url, method: "GET", cookies: cookies}
+
+ return rbbt.insist_request(params)
 }
 
 KB.list_parents = function(database, list){
  return list.get().then(function(list_info){
    var url = '/knowledge_base/user/' + database + '/collection_parents' 
 
-   //url = add_parameter(url, 'collection', JSON.stringify(collection))
-   //return m.request({url: url, method: "POST", data:{collection:collection}})
-   //url = add_parameter(url, '_format', 'tsv_json')
-   //return rbbt.post(url, {collection: collection})
-   
    var collection = {}
    collection[list.type] = list_info.entities