rbbt-rest 1.7.17 → 1.7.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 891ff04e00684eafdcbd23d0953988badb7b25b0
-  data.tar.gz: a1ddd85173b784998afb856a21de86a11425663b
+  metadata.gz: 4cb820762ab31ca47b731784cc93f6826d057a79
+  data.tar.gz: e01a21750686b96449e811c9f42d2f01aaa8b00b
 SHA512:
-  metadata.gz: 3ddca2a8ab4fb70d32a0c6ae5a8430e58a9457b113c4e160888ebefecb9a399ef5ff8cdbd68f6907af42af75bd1636c3d3174d84b7422ed751ed21a0114993a7
-  data.tar.gz: 97fde0bd9ba78bcd376e7be62f69ed85c86820ad5d6087a3fd26906a6f03468ef58a5a4e40d5c994722345a5c7ab8ee7850263755d4cda8888443456f5bdf332
+  metadata.gz: 43c411823107dd3b10a869354bcaee32c0e227cf4165e641c3936a19a0825f2f4b5c3c2a8b8c74369731511ff1d540ff259e8eda6666dd5512985e032f698f62
+  data.tar.gz: 88ecd5856f8550634fc58a134bb522025fe2e26a596350bdbec4eb373a533dad804f4ff004449ef08c9e8397f88da55ca60777aa6a244bd330cb1b8dd11b6c49

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

@@ -166,6 +166,7 @@ module RbbtRESTHelpers
           begin
             check_step step
           rescue Aborted
+            step.clean
             raise RbbtRESTHelpers::Retry
           end
 

data/lib/rbbt/rest/entity.rb

@@ -460,8 +460,29 @@ module Sinatra
 
           entity = setup_entity(entity_type, entity, @clean_params)
 
-          content_type "application/json"
-          halt 200, entity.send(property,*args).to_json
+          begin
+            res = entity.send(property,*args)
+          rescue
+            if entity.respond_to?(:format) and  entity.base_type.respond_to?(:default_format) and entity.format != entity.base_type.default_format
+              entity = entity.to(:default)
+              Log.warn "Error computing property #{property} for #{entity}. Automatically changing entity format to default"
+              retry
+            else
+              raise $!
+            end
+          end
+
+          case res
+          when String
+            content_type "application/json"
+            halt 200, '"' + res + '"'
+          when Fixnum
+            content_type :text
+            halt 200, res.to_s
+          else
+            content_type "application/json"
+            halt 200, res.to_json
+          end
         end
 
         get '/entity_list_property/:property/:entity_type/:list_id' do
@@ -498,6 +519,52 @@ module Sinatra
           halt 200, list.send(property, *args).to_json
         end
 
+        post '/entity_list_property/:property/:entity_type' do
+          entity_type = consume_parameter :entity_type
+          property = consume_parameter :property
+          list = consume_parameter :list
+          info = consume_parameter :info
+          args = consume_parameter :args
+
+          info = (info.nil? or info.empty?) ? {} : JSON.parse(info)
+          entity_type = Entity::REST.restore_element(entity_type)
+          list = Misc.prepare_entity(list.split(/[,|]/), entity_type, info)
+          list.extend AnnotatedArray
+
+          args = (args.nil? or args.empty?) ? nil : begin JSON.parse(args) rescue args end
+          case args
+          when Hash
+            args = [args] 
+          when String
+            args = args.split(/[,\|]/)
+          end
+
+          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
+              list = list.to(:default)
+              Log.warn "Error computing property #{property} for list. Automatically changing list format to default"
+              retry
+            else
+              raise $!
+            end
+          end
+
+          case res
+          when String
+            content_type "application/json"
+            halt 200, '"' + res + '"'
+          when Fixnum
+            content_type :text
+            halt 200, res.to_s
+          else
+            content_type "application/json"
+            halt 200, res.to_json
+          end
+        end
+
+
 
         #{{{{{{{{{{{{{{
         #{{{ FAVOURITES

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

@@ -39,6 +39,9 @@ module EntityRESTHelpers
     params = {} if params.nil?
     locals = {:entity => entity}.merge(params)
 
+    name = entity.respond_to?(:name)? entity.name : entity
+    @title = "#{name} [#{$title}]"
+
     layout_file = layout ? locate_template("layout") : nil
 
     render(template_file, locals, layout_file, "Entity: #{ entity }")
@@ -49,9 +52,12 @@ module EntityRESTHelpers
 
     locals = params.merge({:entity => entity})
 
+    name = entity.respond_to?(:name)? entity.name : entity
+    @title = "#{action} #{name} [#{$title}]"
+
     layout_file = layout ? locate_template("layout") : nil
 
-    render(template_file, locals, layout_file, "Entity #{ action }: #{ entity }")
+    render(template_file, locals, layout_file, "Action #{ action }: #{ entity }")
   end
 
   def entity_list_render(list, id)
@@ -59,6 +65,9 @@ module EntityRESTHelpers
 
     locals = {:list => list, :list_id => id}
 
+    name = id
+    @title = "#{name} [#{$title}]"
+
     layout_file = layout ? locate_template("layout") : nil
 
     render(template_file, locals, layout_file, "Entity list: #{ id }")
@@ -69,9 +78,12 @@ module EntityRESTHelpers
 
     locals = params.merge({:list => list, :list_id => id})
 
+    name = id
+    @title = "#{action} #{name} [#{$title}]"
+
     layout_file = layout ? locate_template("layout") : nil
 
-    render(template_file, locals, layout_file, "Entity list #{ action }: #{ id }")
+    render(template_file, locals, layout_file, "Action #{ action } for list: #{ id }")
   end
 
   def entity_map_render(map_id, type, column)
@@ -80,6 +92,9 @@ module EntityRESTHelpers
     map = Entity::Map.load_map(type, column, map_id, user)
     locals = {:map => map, :map_id => map_id}
 
+    name = map_id
+    @title = "#{name} [#{$title}]"
+
     layout_file = layout ? locate_template("layout") : nil
 
     render(template_file, locals, layout_file, "Entity map: #{ map_id }")
@@ -90,9 +105,12 @@ module EntityRESTHelpers
 
     locals = params.merge({:map => map, :map_id => id})
 
+    name = id
+    @title = "#{action} #{name} [#{$title}]"
+
     layout_file = layout ? locate_template("layout") : nil
 
-    render(template_file, locals, layout_file, "Entity map #{ action }: #{ id }")
+    render(template_file, locals, layout_file, "Action #{ action } for map: #{ id }")
   end
 
 

data/lib/rbbt/rest/main.rb

@@ -69,12 +69,11 @@ module Sinatra
         before do
           method = request.request_method
           method_color = case method
-
-          when "GET"
-            :cyan
-          when "POST"
-            :yellow
-          end
+                         when "GET"
+                           :cyan
+                         when "POST"
+                           :yellow
+                         end
 
           Log.medium{ "#{Log.color method_color, method} #{Log.color(:blue, request.ip)}: " << request.path_info.gsub('/', Log.color(:blue, "/")) << ". Params: " << Log.color(:blue, Misc.fingerprint(params))}
           process_common_parameters
@@ -88,12 +87,13 @@ module Sinatra
 
         after do
           method = request.request_method
+
           method_color = case method
-          when "GET"
-            :cyan
-          when "POST"
-            :green
-          end
+                         when "GET"
+                           :cyan
+                         when "POST"
+                           :green
+                         end
 
           status = response.status.to_s
           case status.to_i

data/lib/rbbt/rest/workflow.rb

@@ -174,7 +174,7 @@ module Sinatra
         job = workflow.load_id(File.join(task, job))
 
         begin
-          check_step job
+          check_step job unless job.done?
         rescue Aborted
         end
 

data/share/views/compass/app.sass

@@ -27,6 +27,7 @@ a.entity
 .action_parameters
   form > .field
     margin-bottom: 2em !important
+    margin: auto
   input[type=file]
     display:inline-block
   span.file_or_text_area

data/share/views/compass/layout.sass

@@ -45,6 +45,8 @@ body
   overflow: auto
 
 @media #{$only-large}
+  #top_menu > .item.title
+    margin-left: 32px
   #top_menu > .favourite
     white-space: nowrap
 
@@ -145,9 +147,9 @@ body
 
   #content
     margin-top: 2em
-    margin-left: 0.5em !important
-    margin-right: 0.5em !important
-    width: calc(100% - 2 * 0.5em)
+    margin-left: 16px !important
+    margin-right: 16px !important
+    width: calc(100% - 2 * 16px)
     padding: 0px
 
   .entity_card, .entity_list_card

data/share/views/compass/misc.sass

@@ -54,8 +54,11 @@ table, table.responsive
 .table_column_selector
   span.field
     font-size: 1.2em
-    width: 10em
+    width: 15em
     display: inline-block
+    overflow: hidden
+    text-overflow: ellipsis
+    margin-right: 2em
 
 .figure
   margin-bottom: 1em
@@ -207,3 +210,16 @@ td
 span.choice
   padding: 0.5em
   cursor: pointer
+
+ul.tasks
+  li 
+    a
+      margin-right: 1em
+      overflow: hidden
+      text-overflow: ellipsis
+
+.modal 
+  .error.message
+    ul.stacktrace
+      li > span
+        margin-left: 0.5em

data/share/views/entity/Default.haml

@@ -11,7 +11,7 @@
 - if entity.respond_to? :genes
   - genes = entity.genes
   - list_container = ListContainer.new
-  - list_container.add "Genes for #{[entity.base_type, name] * ": "}", genes
+  - list_container.add "#{name} #{entity.base_type} genes", genes
   - entity_card.list_container = list_container
 
 - entity_card.action_controller = default_action_controller entity

data/share/views/form.haml

@@ -14,18 +14,18 @@
         :markdown
           #{task_info[:description]}
 
-  .form.action_parameters
+  .form.action_parameters.ui.segment
     = partial_render('partials/form', :id => id, :action => action, :method => 'post', 
       :enctype => "multipart/form-data", :info => task_info, :klass => 'workflow_task')
 
   - if workflow.libdir.examples[task.to_s].exists?
     .examples
-
-      Click below to load example data:
-        
       :javascript
         example_inputs = [];
-      %ul
+
+      Click to load example data:
+        
+      %ul.ui.buttons
         - workflow.libdir.examples[task.to_s].glob('*').each do |example_dir|
           - name = File.basename(example_dir)
           - task_info = workflow.task_info task
@@ -33,7 +33,7 @@
           - inputs.each{ |k,v| v.replace Open.read(v) if String === v and File.exists? v }
           :javascript
             example_inputs["#{ name }"] = #{inputs.to_json}
-          %li
+          %li.ui.button
             %a.load_example(href="#" task=task name=name)= name
 
       :javascript

data/share/views/layout/header.haml

@@ -4,7 +4,7 @@
 
 %link{:rel => "icon", :type => "image/gif", :href => "/favicon.gif"}/
 
-%title= $title
+%title= @title || $title
 
 // Semantic-ui
 
@@ -62,10 +62,10 @@
 - %w(dom_update fragment actions table list map reveal).each do |file|
   - record_js "/js-find/rbbt/#{ file }"
 
-- %w(rbbt rbbt.basic rbbt.exception rbbt.job rbbt.page rbbt.entity rbbt.entity_list rbbt.entity_map rbbt.views rbbt.favourites rbbt.modal).each do |file|
+- %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).each do |file|
+- %w(rbbt.knowledge_base rbbt.aesthetics rbbt.plots rbbt.aes_plots).each do |file|
   - record_js "/js-find/#{ file }"
 
 - record_js "/js-find/app"

data/share/views/layout/top_menu.haml

@@ -1,5 +1,5 @@
 #top_menu.ui.fixed.menu
-  .item
+  .item.title
     %a.header(href='/')= $title
 
 

data/share/views/partials/form.haml

@@ -27,7 +27,7 @@
     %div(class="field #{types[input]} #{input} #{hide ? 'hide' : ''}")
       - input_options = options[input]
       - input_options = input_options.dup unless input_options.nil?
-      != form_input(input, types[input], defaults[input], values[input], descriptions[input], input_id, input_options)
+      !~ form_input(input, types[input], defaults[input], values[input], descriptions[input], input_id, input_options)
 
 
   .input.field.submit

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

@@ -0,0 +1,381 @@
+rbbt.plots.aes = {}
+
+rbbt.plots.aes.get_properties = function(list, rules){
+  if (undefined === rules) rules == []
+  if (undefined === list.properties) list.properties = {}
+  var promises = []
+  forArray(rules, function(rule){
+    var name = rule.name
+    var extract = rule.extract
+    
+    if (rule.entity_type && rule.entity_type != list.type) return 
+
+    if (rule.info){
+      var property = rule.property
+      var deferred = m.deferred()
+      var entry = rule.info
+      if (undefined === name) name = entry
+
+      var value = list.info[entry]
+      if (undefined === value && entry == 'type') value = list.type
+      if (undefined === value && entry == 'code') value = list.codes
+
+      deferred.resolve(value)
+      promise = deferred.promise
+    }
+
+    if (rule.value){
+      var property = rule.property
+      var deferred = m.deferred()
+      deferred.resolve(rule.value)
+      promise = deferred.promise
+    }
+
+    if (rule.property){
+      var property = rule.property
+      var args = rule.args
+      if (undefined === name) name = property
+      promise = rbbt.entity_array.property(list.codes, list.type, list.info, property, args)
+      if (extract){ promise = promise.then(function(res){ return res.map(extract)}) }
+    }
+
+    if (rule.workflow){
+      var workflow = rule.workflow
+      var task = rule.task
+      var args = rule.args
+      if (undefined === name) name = task
+      promise = rbbt.job(workflow, task, args, true)
+      if (extract){ promise = promise.then(function(res){ return list.codes.map(function(code){return extract.call(null, res, code)}) } )}
+    }
+
+    if (rule.parents || rule.children){
+      var kb_type 
+      var database
+      if (rule.parents){
+        kb_type = 'parent'
+        var database = rule.parents
+        if (undefined === name) name = database
+
+        promise = rbbt.entity_array.parents(list.codes, list.type, database)
+      }else{
+        kb_type = 'children'
+        var database = rule.children
+        if (undefined === name) name = database
+
+        promise = rbbt.entity_array.children(list.codes, list.type, database)
+      }
+
+      if (rule.field){
+        promise = m.sync([promise,rbbt.knowledge_base.database_info(database)]).then(function(res){
+          var data = res[0]
+          var db_info = res[1]
+          var fields = db_info.fields
+          var field_pos = fields.indexOf(rule.field)
+
+          if (field_pos < 0){
+            var msg = "Field not found: " + rule.field + ". Options: " + fields.join(", ")
+            throw new Error(msg)
+          }
+
+          var matches = {}
+          forHash(data, function(key, values){
+            var source = values[0]
+            var target = values[1]
+            if (matches[source] === undefined) matches[source] = {}
+            matches[source][target] = values[field_pos+2]
+          })
+          return matches
+        })
+      }else{
+        promise = promise.then(function(data){
+          var matches = {}
+          forHash(data, function(key, values){
+            var source = values[0]
+            var target = values[1]
+            if (matches[source] === undefined) matches[source] = {}
+            matches[source][target] = values.slice(2) 
+          })
+          return matches
+        })
+      }
+
+      if (extract){
+        promise = promise.then(function(matches){
+          return list.codes.map(function(e){ 
+            return extract.call(null, matches, e)
+          })
+        })
+      }
+      else{
+        promise = promise.then(function(matches){
+          return list.codes.map(function(e){ return matches[e] })
+        })
+      }
+    }
+
+    promises.push(promise.then(function(res){list.properties[name] = res}))
+  })
+
+  return m.sync(promises)
+}
+
+rbbt.plots.aes.set_aes = function(list, aes_rules){
+  if (undefined === list.aes) list.aes = {}
+  forArray(aes_rules, function(rule){
+
+    if (rule.entity_type && rule.entity_type != list.type) return 
+
+
+    var name = rule.name
+    var aes = rule.aes
+    var mapper = rule.mapper
+    var mapper_obj = rule.mapper_obj
+    var property = list.properties[name]
+
+    if (rule.value){
+      list.aes[aes] = rule.value
+      return 
+    }
+
+    if (undefined === property && list.info[name]) property = list.info[name]
+    if (undefined === property && name == 'type') property = list.type
+    if (undefined === property && name == 'code') property = list.codes
+    if (undefined === property) return
+
+    list.aes[aes] = aes_module.map_aesthetic(property, mapper, mapper_obj)
+  })
+}
+
+rbbt.plots.aes.update_aes = function(graph_model){
+  var data_promises = []
+  forHash(graph_model.entities, function(type, list){
+    data_promises.push(
+
+      rbbt.plots.aes.get_properties(list, graph_model.rules).
+        then(function(){
+      rbbt.plots.aes.set_aes(list, graph_model.aes_rules)
+        })
+
+    )
+  })
+
+  forHash(graph_model.associations, function(db, list){
+    data_promises.push(
+
+      rbbt.plots.aes.get_properties(list, graph_model.edge_rules).
+        then(function(){
+      rbbt.plots.aes.set_aes(list, graph_model.edge_aes_rules)
+        })
+
+    )
+  })
+  return m.sync(data_promises)
+}
+
+//{{{ SUBSET
+rbbt.plots.aes.subset = function(db,source,target){
+  var promise = rbbt.entity_array.subset(db,source,target)
+  var db_info = KB.database_info(db)
+  return m.sync([promise,db_info]).then(function(d){
+    var associations = d[0]
+    var info = d[1]
+    var fields = ['source', 'target'].concat(info.fields)
+
+    var edges = {}
+    edges.codes = []
+    edges.database = db
+    edges.source_type = info.source
+    edges.target_type = info.target
+    edges.source_info = info.source_entity_options
+    edges.target_info = info.target_entity_options
+    edges.info = {}
+    edges.info.database = db
+    edges.properties = {}
+    edges.aes = {}
+
+    for (i in fields)
+      edges.info[fields[i]] = []
+
+    forHash(associations, function(code, values){
+      edges.codes.push(code)
+      for(i in values){
+        var field = fields[i]
+        var value = values[i]
+        edges.info[field].push(value)
+      }
+    })
+
+    edges.aes['source'] = edges.info['source']
+    edges.aes['target'] = edges.info['target']
+    edges.aes['database'] = db
+
+    return edges
+  })
+}
+
+//{{{ CONSOLIDATION
+
+rbbt.plots.aes.consolidate_list = function(list){
+  var nodes = []
+
+  var codes = list.codes
+  var info = list.info
+  var aes = list.aes
+  var properties = list.properties
+
+  for (i in codes){
+    var node = {}
+    node.code = codes[i]
+    forHash(aes, function(name, values){
+      var value
+      if (typeof values == 'object') value = values[i]
+        else value = values
+          node[name]  = value
+    })
+    nodes.push(node)
+  }
+
+  return nodes
+}
+
+rbbt.plots.aes.consolidate_associations = function(list, database){
+  var edges = []
+  forHash(list,function(code, values){
+    var edge = {}
+    var source_code = values[0]
+    var target_code = values[1]
+
+    edge.source = source_code
+    edge.target = target_code
+    edge.database = database
+
+    edges.push(edge)
+  })
+
+  return edges
+}
+
+rbbt.plots.aes.consolidate_associations = function(list){
+  var nodes = []
+
+  var codes = list.codes
+  var info = list.info
+  var aes = list.aes
+  var properties = list.properties
+  var values = list.properties
+
+  for (i in codes){
+    var node = {}
+    node.code = codes[i]
+    forHash(aes, function(name, values){
+      var value
+      if (typeof values == 'object') value = values[i]
+        else value = values
+          node[name]  = value
+    })
+    nodes.push(node)
+  }
+
+  return nodes
+}
+
+rbbt.plots.aes.consolidate = function(graph_model){
+  var model = {}
+
+  var nodes = []
+
+  forHash(graph_model.entities, function(type, list){
+    var list_nodes = rbbt.plots.aes.consolidate_list(list)
+    for (i in list_nodes) nodes.push(list_nodes[i])
+  })
+
+  var edges = []
+  forHash(graph_model.associations, function(database, list){
+    var list_edges = rbbt.plots.aes.consolidate_associations(list,database)
+    for (i in list_edges) edges.push(list_edges[i])
+  })
+
+  model.nodes = nodes
+  model.edges = edges
+
+  return model
+}
+
+//}}} CONSOLIDATION
+
+
+rbbt.plots.aes.build_d3 = function(graph_model){
+
+  var model = rbbt.plots.aes.consolidate(graph_model)
+
+  var node_index = {}
+  for (i=0; i< model.nodes.length; i++) node_index[model.nodes[i].code] = i
+
+  for (i=0; i< model.edges.length; i++){
+    var edge = model.edges[i]
+    edge.source = node_index[edge.source]
+    edge.target = node_index[edge.target]
+  }
+
+  model.links = model.edges
+  model.edges = undefined
+  model.node_index = node_index
+
+  return model
+}
+
+rbbt.plots.aes.build_cytoscape = function(graph_model){
+  var model = rbbt.plots.aes.consolidate(graph_model)
+
+  var dataSchema = {nodes: [], edges:[]}
+
+  var node_vars = {}
+  for (i in model.nodes){
+    for (p in model.nodes[i]){
+      if (undefined !== model.nodes[i][p])
+        node_vars[p] = typeof model.nodes[i][p]
+    }
+  }
+  for (p in node_vars){
+    dataSchema.nodes.push({name: p, type: node_vars[p]})
+  }
+
+  node_vars = {}
+  for (i in model.edges){
+    for (p in model.edges[i]){
+      if (undefined !== model.edges[i][p])
+        node_vars[p] = typeof model.edges[i][p]
+    }
+  }
+  for (p in node_vars){
+    dataSchema.edges.push({name: p, type: node_vars[p]})
+  }
+
+  var cy_model = {}
+  cy_model.dataSchema = dataSchema
+  cy_model.data = model
+
+  return cy_model
+}
+
+rbbt.plots.aes.build_cytoscapejs = function(graph_model){
+  var model = rbbt.plots.aes.consolidate(graph_model)
+
+  var nodes = []
+  forArray(model.nodes, function(node){
+    nodes.push({data: node})
+  })
+
+  console.log(model.edges)
+  var edges = []
+  forArray(model.edges, function(edge){
+    edges.push({data: edge})
+  })
+
+  var cy_model = {}
+  cy_model.elements = {nodes: nodes, edges: edges}
+
+  console.log(cy_model)
+  return cy_model
+}
+