rbbt-rest 1.7.1 → 1.7.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8c139ee7ae135774da4d4aa3f19b32c555cc2e31
-  data.tar.gz: ec59edba9570e29d45712ebac290836885af5bf5
+  metadata.gz: 59c0ed2d456a49f6418d29a6264603d9975f739d
+  data.tar.gz: 3886dd197d5d6b6ea33f471c3edca6397fc682ae
 SHA512:
-  metadata.gz: 86574f5cd8fc1afc2bc10a543335a58b5a68e6017207156d7d14fbcb3a6a20a243ef62990d38bb67cbf01c0326c8d70e04c1c872ce6c553008ce2150ff3335ef
-  data.tar.gz: 9c99fac76fea29fd8d9bcee055eb8ebc120ca872af6ab34781e532dbddcc22ee8b65a9cd396939016cb2217512b78317c7ec7a39d339a25b51b60d28bdcc922b
+  metadata.gz: 58719858ad8424352f9ba49bded0b74e8d466e1d382aba478366e02e646a2fd807e43b2617ac5a4f3d8c4518c0f96841242d82a2d11b45b9d18bc424fe7b058b
+  data.tar.gz: 40ba3da4b639c982216228cf61f5286543ceb7d5aa335617154ccc3a9b3b6be145b67f5fcace57971cf866a51c9ecd6d3653082f4f7e9a018a21bebfb4fb539a

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

@@ -25,6 +25,7 @@ module RbbtRESTHelpers
 
       result = render template_file, {:job => job}, layout_file
 
+      content_type :html
       halt code, result
     else
       content_type :text

data/lib/rbbt/rest/main.rb

@@ -195,7 +195,6 @@ module Sinatra
           raise e unless @format == :html
 
           content_type "text"
-
           halt 500, [e.class.to_s, e.message] * " => " << "\n\n" << (e.backtrace * "\n").gsub('`',"'")
         end
 

data/share/views/compass/app.sass

@@ -419,6 +419,5 @@ body
 
 td
   &.true
-    color: green
-  &.false
-    color: red
+    font-weight: bold
+

data/share/views/partials/table/filters.haml

@@ -21,4 +21,5 @@
       - *Numeric comparison*: lower of grater than (e.g. `< 0.1` or `>= 2`)
       - *Names*: for entities with names, such as genes or pathways; regular expression accepted (e.g. `:name: SF3B1` or `:name: /CDK\d/`)
       - *Length*: for lists (e.g. `:length: > 2`)
+      - *Negation*: Any of the rules above can be negated by prepending the `!` character (e.g. `!:name:/^IG/`)
 

data/share/views/public/js/app.js

@@ -1,7 +1,7 @@
 function fit_content(){
  var height = window.innerHeight - $('footer').outerHeight(true);
  var top_offset = $('#content').get()[0].offsetTop
- $('#content').css('min-height', height - top_offset)
+ $('#content').css('min-height', height - top_offset - 48)
  $('#top_menu dl.rbbt_menu').css('max-height', height - 100)
 }
 

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

@@ -49,22 +49,22 @@ aes_module.get_list_aesthetics = function(list, rules) {
       promise = list.property(rule.property, args)
 
       if (undefined === extract){
-        promises.push(promise.then(result[aes]))
+        promises.push(promise.then(result[aes], rbbt.exception.report))
       }else{
-        promises.push(promise.then(function(v){return v.map(extract)}).then(result[aes]))
+        promises.push(promise.then(function(v){return v.map(extract)}).then(result[aes], rbbt.exception.report))
       }
     }
 
     if (rule.workflow){
       promise = rbbt.job(rule.workflow, rule.task, args,true)
       if (undefined === extract){
-        promises.push(promise.then(result[aes]))
+        promises.push(promise.then(result[aes], rbbt.exception.report))
       }else{
         promises.push(m.sync([list.get(), promise]).then(function(res){
           list_info = res[0]
           data = res[1]
           return list_info.entities.map(function(e){ return extract.call(null, data, e) })
-        }).then(result[aes]))
+        }).then(result[aes], rbbt.exception.report))
       }
     }
 
@@ -108,7 +108,7 @@ aes_module.get_list_aesthetics = function(list, rules) {
       mapped_result[aes] = rbbt.aesthetics.map_aesthetic(values(), mapper)
     })
     return mapped_result
-  }).then(function(){ deferred.resolve(mapped_result) })
+  }).then(function(){ deferred.resolve(mapped_result) }, rbbt.exception.report)
 
   return deferred.promise
 }

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

@@ -1,4 +1,3 @@
-
 rbbt.mlog = function(data){
   console.log(data)
 }
@@ -12,19 +11,29 @@ rbbt.ajax = function(params){
 }
 
 rbbt.post = function(url, data, params){
-  var formData = new FormData()
+  var request_params
+  if (typeof url === 'object'){
+    request_params = url
+    if (data) request_params.data = data
+  }else{
+
+    if (undefined === params)  params = {}
+    if (undefined === params.url) params.url = url
 
-  if (undefined === params)  params = {}
-  if (undefined === params.method) params.method = 'POST'
-  if (undefined === params.url) params.url = url
-  if (undefined === params.serialize) params.serialize = function(formData) {return formData}
+    request_params = {url: url, method: "POST", data: data, serialize: function(formData){return formData} }
+  }
 
+  if (undefined === request_params.method) request_params.method = 'POST'
+  if (undefined === request_params.serialize) request_params.serialize = function(formData) {return formData}
 
-  forHash(data, function(key,value){
-    formData.append(key, value)
-  })
+  if (request_params.data){
+    var formData = new FormData()
+    forHash(request_params.data, function(key,value){
+      formData.append(key, value)
+    })
+    request_params.data = formData
+  }
 
-  var request_params = {url: url, method: "POST", data: formData, serialize: function(formData){return formData} }
   return rbbt.ajax(request_params)
 }
 
@@ -50,7 +59,7 @@ rbbt.insist_request = function(params, deferred, timeout, missing){
         if (params.data !== undefined && params.data['_update'] !== undefined) params.data['_update'] = undefined
           setTimeout(function(){ m.redraw(); rbbt.insist_request(params, deferred,timeout*2.5) }, timeout)
       }else{ 
-        deferred.reject(new Error(xhr.statusText))
+        deferred.reject(new Error("Status " + xhr.status + " in '" + params.url + "': " + xhr.statusText))
       }
     }
   )

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

@@ -8,11 +8,12 @@ var Entity = function(data){
 
  this.type = data.type
  this.format = data.format
+
  if (undefined === data.info)
    this.info = {}
  else
    this.info = data.info 
- this.info = {}
+
  if (this.format === undefined && this.info !== undefined) this.format = this.info['format']
 
  this.full_type = function(){

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

@@ -29,6 +29,6 @@ rbbt.try = function(func){
 }
 
 rbbt.do_try = function(func){
-  rbbt.try(func)()
+  return rbbt.try(func)()
 }
 

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

@@ -39,7 +39,7 @@ fav_module.toggleFavourite_entity = function(){
  var entity = rbbt.page.entity();
 
  if (fav_module.isFavourite_entity(entity)){
-  rbbt.post({url: '/remove_favourite_entity/' + entity.type + '/' + clean_element(entity.code)}).then(fav_module.update)
+  rbbt.post({url: '/remove_favourite_entity/' + entity.type + '/' + clean_element(entity.code), data: entity.info}).then(fav_module.update)
  }else{
   rbbt.post({url: '/add_favourite_entity/' + entity.type + '/' + clean_element(entity.code), data: entity.info}).then(fav_module.update)
  }

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

@@ -130,16 +130,16 @@ rbbt.plots.association_network = function(nodes, associations){
       indices[entity.id] = i
     }
 
-    var edges = []
+    var links = []
     forHash(associations, function(key,value){
       var source = value[0]
       var target = value[1]
       var source_index = indices[source]
       var target_index = indices[target]
-      edges.push({source: source_index, target: target_index, id: key})
+      links.push({source: source_index, target: target_index, id: key})
     })
 
-    return edges
+    return links
 }
 
 //{{{ BASIC RULES
@@ -183,7 +183,7 @@ rbbt.plots.svg_wrapper = function(objs){
   }
 }
 
-rbbt.plots.tile_obj = function(aes){
+rbbt.plots.card_obj = function(aes){
   var class_names = ""
   var style = jQuery.extend({}, aes);
 
@@ -211,7 +211,7 @@ rbbt.plots.tile_obj = function(aes){
 rbbt.plots.svg_obj = function(aes){
   aes.width = '300px'
   aes.height = '200px'
-  var tile = rbbt.plots.tile_obj(aes)
+  var tile = rbbt.plots.card_obj(aes)
 
   var location = {x: aes.x, y: aes.y}
   if (undefined === location.x) location.x = Math.random() * 1000
@@ -262,7 +262,7 @@ rbbt.plots.d3js_graph = function(graph, object){
   var node = svg.selectAll(".node").data(graph.nodes).enter()
       .append("foreignObject").attr("class", "node")
         .attr('width',xsize)
-        .attr('height',ysize).html(function(d){ return mrender(rbbt.plots.tile_obj(d)) })
+        .attr('height',ysize).html(function(d){ return mrender(rbbt.plots.card_obj(d)) })
       .call(force.drag)
 
 
@@ -336,7 +336,7 @@ rbbt.plots.d3js_group_graph = function(graph, object){
   var node = svg.selectAll(".node").data(graph.nodes).enter()
       .append("foreignObject").attr("class", "node")
         .attr('width',xsize)
-        .attr('height',ysize).html(function(d){ return mrender(rbbt.plots.tile_obj(d)) })
+        .attr('height',ysize).html(function(d){ return mrender(rbbt.plots.card_obj(d)) })
       .call(force.drag)
 
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.7.1
+  version: 1.7.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-30 00:00:00.000000000 Z
+date: 2015-10-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake