rbbt-rest 1.6.28 → 1.7.0

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

@@ -6,7 +6,15 @@ rbbt.exception.null = function(variable, text){
 
 rbbt.exception.report = function(err){
   console.log("Error: " + err)
-  rbbt.modal.controller().error(err, "Application Error")
+  var stack = err.stack
+  console.log(stack)
+  if (rbbt.modal){
+    stack = "<ul><li>" + stack.replace(/\n/g, '</li><li>') + '<li/></ul>'
+    stack = stack.replace(/<li><li\/>/g,'').replace(/<li>(.*?)@(.*?):(\d+:\d+)<\/li>/g, '<li>$2<span style="font-weight:bold">$3</span><br/><em>$1</em></li>')
+    rbbt.modal.controller.error(m('.ui.error.message', [m('.header', err), m('.description', m.trust(stack))]), "Application Error")
+  }else{
+    console.log(stack)
+  }
 }
 
 rbbt.try = function(func){

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

@@ -159,9 +159,9 @@ rbbt.Job = function(workflow, task, inputs){
 
 }
 
-rbbt.job = function(workflow, task, inputs){
+rbbt.job = function(workflow, task, inputs,json){
   var job = new rbbt.Job(workflow, task, inputs)
-  return job.run()
+  return job.run(json)
 }
 
 rbbt_job = function(workflow, task, inputs, complete){

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

@@ -23,6 +23,10 @@ rbbt.post.asFormUrlEncoded = function(xhr){
 }
 
 rbbt.log = function(obj){
- console.log(obj)
+  console.log((new Date()).toString() + ' => ' + obj)
 }
 
+rbbt.mount = function(obj, component){
+  obj.className = obj.className + ' mithril-mount'
+  m.mount(obj, component)
+}

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

@@ -14,6 +14,46 @@ KB.parents = function(database, entity){
  return m.request({url: url, method: "GET", type: Entity})
 }
 
+KB.list_parents = function(database, list){
+ return list.get().then(function(list_info){
+   var url = '/knowledge_base/user/' + database + '/collection_parents' 
+
+   collection = {}
+   collection[list.type] = list_info.entities
+   url = add_parameter(url, 'collection', JSON.stringify(collection))
+   url = add_parameter(url, '_format', 'tsv_json')
+   return m.request({url: url, method: "POST"})
+ })
+}
+
+KB.list_children = function(database, list){
+ return list.get().then(function(list_info){
+   var url = '/knowledge_base/user/' + database + '/collection_children' 
+
+   var collection = {}
+   collection[list.type] = list_info.entities
+   var data = {}
+   data.collection = JSON.stringify(collection)
+   data._format = 'tsv_json'
+   
+   return rbbt.post(url, data)
+ })
+}
+
+KB.list_subset = function(database, list, target){
+ return list.get().then(function(list_info){
+   var url = '/knowledge_base/user/' + database + '/subset' 
+
+   var data = {}
+   var source = list_info.entities.join(",")
+   data._format = 'tsv_json'
+   data.source = source
+   if (target) data.target = target.join(",")
+
+   return rbbt.post(url, data)
+ })
+}
+
 Entity.prototype.children = function(database){
  return KB.children(database, this)
 }

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

@@ -1,90 +1,97 @@
-rbbt.modal = {}
-rbbt.modal.element = document.getElementById('modal')
-
-rbbt.modal.vm = (function(){
-  var vm = {}
-  vm.init = function(){
-    console.log(m)
-    vm.visible = m.prop(false)
-    vm.content = m.prop("")
-    vm.title = m.prop("")
-  }
 
-  return vm
-}())
-
-rbbt.modal.controller = function(){
-  var controller = rbbt.modal.controller
-  var vm = rbbt.modal.vm
-  vm.init()
-
-  controller._set = function(content, title){
-    vm.content(content)
-    if (undefined !== title)
-      vm.title(title)
-    else
-      vm.title("")
-    vm.visible(true)
-  }
 
-  controller.show = function(content, title){
-    controller._set(content, title)
-    $(rbbt.modal.element).addClass('active')
-    m.redraw()
-    update_rbbt()
-  }
+ModalComponent = function(element){
+  var component = {}
 
-  controller.error = function(content, title){
-    controller._set(content, title)
-    $(rbbt.modal.element).addClass('active')
-    $(rbbt.modal.element).addClass('error')
-    m.redraw()
-    update_rbbt()
+  component.vm = {
+    element: element,
+    init: function(){ 
+      this.visible = m.prop(false)
+      this.content = m.prop("")
+      this.title = m.prop("")
+    }
   }
 
+  component.controller = function(){
+    var ctrl = component.controller
+    ctrl.vm = component.vm;
+    ctrl.vm.init();
 
-  controller.show_url = function(url, title){
-    if (typeof url == 'string') params = {url: url, method: 'GET',deserialize: function(v){return v}}
-    else params = url
-    vm.visible(true)
-    vm.title("loading")
-    vm.content(m('.ui.loading.basic.segment'))
-    $(rbbt.modal.element).addClass('loading')
-    $(rbbt.modal.element).addClass('active')
-    m.redraw()
-    return rbbt.insist_request(params).then(function(content){
-      $(rbbt.modal.element).removeClass('loading')
-      controller.show(content, title)
-    })
-  }
+    ctrl._set = function(content, title){
+      this.vm.content(content)
+      if (undefined !== title)
+        this.vm.title(title)
+      else
+        this.vm.title("")
+      this.vm.visible(true)
+    }
 
-  controller.close = function(){
-    vm.visible(false)
-    $(rbbt.modal.element).removeClass('error')
-    $(rbbt.modal.element).removeClass('active')
-    m.redraw()
-  }
+    ctrl.show = function(content, title){
+      this._set(content, title)
+      $(this.vm.element).addClass('active')
+      m.redraw()
+      update_rbbt()
+    }
 
-  return controller
-}
+    ctrl.error = function(content, title){
+      this._set(content, title)
+      $(this.vm.element).addClass('active')
+      $(this.vm.element).addClass('error')
+      m.redraw()
+      update_rbbt()
+    }
 
-rbbt.modal.view = function(controller){
-  if (rbbt.modal.vm.visible()){
-    var title
-    if ('object' == typeof rbbt.modal.vm.title()) title = rbbt.modal.vm.title()
-    else title = m.trust(rbbt.modal.vm.title())
+    ctrl.show_url = function(url, title){
+      if (typeof url == 'string') params = {url: url, method: 'GET',deserialize: function(v){return v}}
+      else params = url
 
-    var content
-    if ('object' == typeof rbbt.modal.vm.content()) content = rbbt.modal.vm.content()
-    else content = m.trust(rbbt.modal.vm.content())
+      this.vm.visible(true)
+      this.vm.title("loading")
+      this.vm.content(m('.ui.loading.basic.segment'))
+      $(this.vm.element).addClass('loading')
+      $(this.vm.element).addClass('active')
+      m.redraw()
+      return rbbt.insist_request(params).then(function(content){
+        $(ctrl.vm.element).removeClass('loading')
+        ctrl.show(content, title)
+      })
+    }
 
+    ctrl.close = function(){
+      ctrl.vm.visible(false)
+      $(ctrl.vm.element).removeClass('error')
+      $(ctrl.vm.element).removeClass('active')
+      m.redraw()
+    }
 
-    var header = [title, rbbt.mview.ibutton({onclick: rbbt.modal.controller.close, class:'small close', style: 'margin-top: -4px'}, m('i.icon.close'))]
-    var modal_content = [m('.header', header), m('.content', content)]
-    return modal_content
-  }else{
-    return ""
+    return ctrl
   }
+
+  component.view = function(ctrl){
+    if (ctrl.vm.visible()){
+      var title
+      if ('object' == typeof ctrl.vm.title()) title = ctrl.vm.title();
+      else title = m.trust(ctrl.vm.title());
+
+      var content
+      if ('object' == typeof ctrl.vm.content()) content = ctrl.vm.content();
+      else content = m.trust(ctrl.vm.content());
+
+
+      var header = [title, rbbt.mview.ibutton({onclick: ctrl.close, class:'small close', style: 'margin-top: -4px'}, m('i.icon.close'))];
+      var modal_content = [m('.header', header), m('.content', content)];
+      return modal_content;
+    }else{
+      return "";
+    }
+  }
+
+
+  return component;
 }
 
-if (rbbt.modal.element) m.module(rbbt.modal.element, rbbt.modal)
+if (document.getElementById('modal')){
+  rbbt.modal = new ModalComponent(document.getElementById('modal'))
+
+  m.mount(document.getElementById('modal'), rbbt.modal)
+}

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

@@ -0,0 +1,276 @@
+rbbt.plots = {}
+
+rbbt.plots.list_plot = function(list, rules, create_obj){
+  var component = {}
+  component.create_obj = create_obj
+
+  component.vm = {
+    list: list,
+    rules: rules,
+
+    node_aesthetics: m.prop(),
+    update_aesthetics: function(){
+      rbbt.log('update-aesthetics')
+      //return rbbt.aesthetics.get_list_aesthetics(component.vm.list,component.vm.rules)
+      rbbt.aesthetics.get_list_aesthetics(component.vm.list,component.vm.rules)
+                 .then(component.vm.node_aesthetics).then(component.vm.update_nodes)
+      m.redraw()
+    },
+
+    nodes: m.prop(),
+    no_layout: m.prop(false),
+    update_nodes: function(node_aesthetics){
+      rbbt.log('update-nodes')
+      var deferred = m.deferred()
+
+      component.vm.list.get().then(function(list_info){
+        var aes = list_info.entities.map(function(entity, i){
+          var e_aes = {id: entity, index: i}
+          forHash(node_aesthetics, function(key, value){
+            e_aes[key] = value[i]
+          })
+          return e_aes
+        })
+        rbbt.log('update-nodes:done')
+        return aes
+      }).then(component.vm.nodes).then(component.vm.update_layout).then(deferred.resolve)
+      return deferred.promise
+    },
+
+    associations: m.prop(),
+    graph: function(){
+      if (undefined === component.vm.associations() || undefined === component.vm.nodes()) return {links:[],nodes:[]}
+      var links = rbbt.plots.association_network(component.vm.nodes(), component.vm.associations())
+      var graph = {links: links, nodes: component.vm.nodes()}
+      return(graph)
+    },
+    update_layout: function(nodes){
+      rbbt.log('update-layout')
+
+      if (component.vm.no_layout() || undefined === component.vm.associations()){
+        var deferred = m.deferred()
+        deferred.resolve(nodes)
+        return deferred.promise
+      }
+
+      rbbt.log('update-layout:force')
+
+      return rbbt.plots.force_layout(component.vm.graph()).then(function(graph){return graph.nodes})
+    },
+
+    init: function(){ 
+      rbbt.log('init')
+      component.vm.update_aesthetics()
+    },
+  }
+
+  component.controller = function(){
+    var ctrl = this
+    this.vm = component.vm;
+    this.vm.init()
+    this.onunload = function() {
+      console.log("unloading component");
+    }
+  }
+
+  component.wrapper = function(objs){
+    if (undefined === objs){
+      rbbt.log("Loading")
+      return m('.ui.basic.segment.plot.loading', "Loading")
+    }else{
+      rbbt.log("Wrap")
+      return m('.ui.basic.segment.plot', objs)
+    }
+  }
+
+  component.view = function(ctrl){
+    rbbt.log('View')
+    if (ctrl.vm.nodes()){
+      var objs = ctrl.vm.nodes().map(function(aes,i){
+        return component.create_obj(aes)
+      })
+      return component.wrapper(objs)
+    }else{
+      return component.wrapper()
+    }
+  }
+
+  return component;
+}
+
+//{{{ PLOTS
+
+
+//{{{ FORCE LAYOUT
+
+rbbt.plots.force_layout = function(graph){
+  var deferred = m.deferred()
+  m.startComputation()
+  rbbt.log("force-start")
+  var force = d3.layout.force()
+    .charge(-5200)
+    .linkDistance(5000)
+    .size([10000, 10000])
+    .nodes(graph.nodes)
+    .links(graph.links)
+    .start();
+
+  force.on("end", function() {
+    m.endComputation()
+    rbbt.log("force-end")
+    deferred.resolve(graph)
+  })
+  return deferred.promise
+}
+
+rbbt.plots.association_network = function(nodes, associations){
+    var indices = {}
+    for (i = 0; i < nodes.length; i++){
+      var entity = nodes[i]
+      indices[entity.id] = i
+    }
+
+    var edges = []
+    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})
+    })
+
+    return edges
+}
+
+//{{{ BASIC RULES
+
+
+rbbt.plots.basic_rules = function(study){
+  var rules = []
+  rules.push({aes:'label', property: 'link', extract: m.trust})
+  rules.push({aes:'description', property: 'long_name'})
+  rules.push({aes:'highlight', property: 'significant_in_study', args:study})
+  rules.push({aes:'order', property: 'damage_bias_in_study', args:study})
+  rules.push({aes:'color_class', workflow: 'GEO', task: 'differential', args:{threshold: 0.05, dataset: 'GSE13507', to_gene: true, main:"/Primary/", contrast: "/ontrol/"}, extract: function(result, entity){
+    if (undefined === result[entity]) return ""
+    var pvalue = result[entity][result[entity].length-1]
+    if (pvalue > 0 && pvalue < 0.05){
+      return "green"
+    }else{
+      if (pvalue < 0 && pvalue > -0.05){
+        return "red"
+      }else{
+        return ""
+      }
+    }
+  }})
+  rules.push({aes:'color', workflow: 'GEO', task: 'differential', mapper: 'sign-gradient', args:{threshold: 0.05, dataset: 'GSE13507', to_gene: true, main:"/Primary/", contrast: "/ontrol/"}, extract: function(result, entity){
+    if (undefined === result[entity]) return ""
+    var pvalue = result[entity][result[entity].length-1]
+    return pvalue_score(pvalue)
+  }})
+
+  return rules
+}
+
+rbbt.plots.svg_wrapper = function(objs){
+  if (undefined === objs){
+    return m(".ui.basic.segment.loading", "Loading")
+  }else{
+    var cell_svg = m('image',{"xlink:href": 'https://upload.wikimedia.org/wikipedia/commons/1/1a/Biological_cell.svg',x:0,y:0,height:100, width:100})
+    objs.unshift(cell_svg)
+    return m("svg[height='800px'][width='100%'][viewPort='0 0 10000 10000'][xmlns:xlink='http://www.w3.org/1999/xlink']",{config: svgPanZoom}, objs)
+  }
+}
+
+rbbt.plots.tile_obj = function(aes){
+  var class_names = ""
+
+  if (aes.color_class){
+    class_names = class_names + ' ' + aes.color_class
+    aes.color_class = undefined
+  }
+
+  var title = aes.label
+  if (aes.highlight)
+    title = [m('i.icon.star',{style:"display:inline;font-size:1em"}), title]
+
+  var content = aes.description
+
+  var header = m('.ui.header', title)
+  var colors = m('.ui.segment', {"style":"background-color:" + aes.color})
+  aes.color = undefined
+  var body = m('.ui.description',[content, colors])
+
+  return m('.tile.ui.segment', {style: aes, class: class_names}, 
+    [header, body]
+  )
+}
+
+rbbt.plots.svg_obj = function(aes){
+  aes.width = '300px'
+  aes.height = '200px'
+  var tile = rbbt.plots.tile_obj(aes)
+
+  var location = {x: aes.x, y: aes.y}
+  if (undefined === location.x) location.x = Math.random() * 1000
+  if (undefined === location.y) location.y = Math.random() * 1000
+  location.width = aes.width
+  location.height = aes.height 
+  location.requiredExtensions="http://www.w3.org/1999/xhtml"
+  location.class="node"
+
+  return m('foreignObject', location, m('body[xmlns="http://www.w3.org/1999/xhtml"]',tile))
+}
+
+rbbt.plots.d3js_graph = function(graph, object){
+  var xsize = 300, ysize = 200
+  var width = 1200
+      height = 800
+
+  var color = d3.scale.category20();
+
+  var svg = d3.select(object)
+      .attr("width", "100%")
+      .attr("height", height)
+
+  var force = d3.layout.force()
+      .charge(-20*xsize)
+      .linkDistance(3*xsize)
+      .size([width, height])
+      .nodes(graph.nodes)
+      .links(graph.links)
+
+  force.start()
+  force.on("tick", function() {
+    link.attr("x1", function(d) { return d.source.x + xsize/2; })
+        .attr("y1", function(d) { return d.source.y + ysize/2; })
+        .attr("x2", function(d) { return d.target.x + xsize/2; })
+        .attr("y2", function(d) { return d.target.y + ysize/2; });
+
+    node.attr("x", function(d) { return d.x; })
+        .attr("y", function(d) { return d.y; });
+  })
+
+  var link = svg.selectAll(".link")
+      .data(graph.links)
+    .enter().append("line")
+      .attr("class", "link")
+      .style("stroke-width", function(d) { return Math.sqrt(d.value); });
+
+  var node = svg.selectAll(".node")
+      .data(graph.nodes)
+    .enter().append("foreignObject").attr('width',xsize).attr('height',ysize).call(force.drag)
+      .attr("class", "node")
+      .html(function(d) { return mrender(rbbt.plots.tile_obj(d)) });
+
+  rbbt.log("force:warmup")
+  for(i=0; i<100; i++) force.tick()
+
+  rbbt.log("force:panZoom")
+  svgPanZoom(object)
+}
+
+rbbt.mrender = function(mobj){
+  return render(mobj)
+}