rbbt-rest 1.1.4 → 1.1.5

checksums.yaml

@@ -1,15 +1,15 @@
 ---
 !binary "U0hBMQ==":
   metadata.gz: !binary |-
-    MjY4NGQ1Mjg4YTIyYmRjYWQ0OWFkMjQ4NmQxMjU3NmIwYjIzN2M1Yw==
+    YmU4OTJhZGMwZTZkYzY0MTcxZjVlNjNlM2QyYjc2YTMyOWIyYjc0MA==
   data.tar.gz: !binary |-
-    MTQ3MGVlMzE3NjU2ZDc3ZmI4YjM4MDA1MjY0ZDI4NjFkYTY5ZDAxOQ==
+    YjIwNDcyMzgzMWViOGY4NTI1ZTM5YjkzZTA5Y2Q1MzdlYjJmNzk4Nw==
 !binary "U0hBNTEy":
   metadata.gz: !binary |-
-    OTg5MGEwZmQ5YmYyOWRmNzM2YjQ4OTZkNzI1YjRiZGQ5ZjkzYWRhMjJjNTVj
-    ZTliMjJlYWE0YjJhOGI1ZTdhZWVkNzM4MjFmODllZGRhZDA2OGE3NjQ1ZDQ5
-    ZTBmYTkyOTY2ZDAxNzlmMGYzYzFiZjY2NmFlN2Q5M2M1OWM1NmU=
+    NmZjNDljMWQxYTc3NTEwYjJkOTgyNWFhNjcyZjI3ODA2YTk4NzYzNTdiZDA1
+    ZjY0MTE1YmQxZDdhMWI2MmRkMmJmNzMxMWQ0MTIyMThlOGY3ODc0Njg4NGY0
+    NzgyYTU4MDcyOTkyYmM3OGE2YjM4MDQ3MTM2ZTkwM2YxYzJkNWE=
   data.tar.gz: !binary |-
-    ZTQ3Y2Q5YTFjOGQ4YTlmMzlhMmJhNTUwZTFlODUxNjhjYjEwNzBmZDg2YmNk
-    OWI2OGQzNzI1MzNmYTQzYzVjYWJlYmZiNWY2NDY5NGRmYWE2OWQ4ZjE4YjBm
-    MDliZDczODJmNjdlYWNiODZiOGY3Mzk3MTFjZGFkMDMzZjBhYTU=
+    ZjVlOGQxMTBkZGY3N2IxYTgwODU3MDc5NmE4OGIyYzMyY2I1NDdhNDc5ODZk
+    NzFlM2FlMDhjMzhlNDU0Y2QzZjJmZjUxOGQyMGM2NmNhN2U2ZWIzMzNmN2Uz
+    MGE0MDZlNDRlMWVjY2U2NTE2ZjRkM2Y3NGE5MGI4OTY2ZTI3OTk=

data/config.ru

@@ -1,6 +1,8 @@
 require 'zurb-foundation'
 require 'modular-scale'
 
+require 'sinatra'
+
 require 'rbbt'
 require 'rbbt/rest/main'
 require 'rbbt/rest/entity'
@@ -95,5 +97,6 @@ end
 
 #{{{ RUN
 $title = "RbbtRest"
+
 use Rack::Deflater
 run RbbtRest

data/lib/rbbt/rest/client.rb

@@ -36,7 +36,11 @@ class WorkflowRESTClient
   def self.get_json(url, params = {})
     Log.debug("RestClient get_json #{}: #{ url } - #{params.inspect}")
     params = params.merge({ :_format => 'json' })
-    res = RestClient.get(url, :params => params)
+    begin
+      res = RestClient.get(url, :params => params)
+    rescue => e
+      raise JSON.parse(e.response)["message"]
+    end
     begin
       JSON.parse(res)
     rescue
@@ -175,6 +179,10 @@ class WorkflowRESTClient
     name
   end
 
+  def workflow_description
+    WorkflowRESTClient.get_raw(File.join(url, 'description'))
+  end
+
   def task_info(task)
     @task_info ||= {}
     @task_info[task]
@@ -301,12 +309,3 @@ class WorkflowRESTClient
     end
   end
 end
-
-if __FILE__ == $0
-  client = WorkflowRESTClient.new("http://darthcaedus:9292/Sequence", "Sequence")
-
-  job = client.job(:genes_at_genomic_positions, "1", :organism => "Hsa", :positions => ["2:198266834:R"]).clean.fork
-  puts job.join.load.to_s
-  
-end
-

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

@@ -14,6 +14,7 @@ module RbbtRESTHelpers
   end
 
   def cache(name, params = {}, &block)
+    @cache_type ||= params[:cache_type] if params[:cache_type]
     return yield if name.nil? or cache_type.nil? or cache_type == :none
 
     send_file = consume_parameter(:_send_file, params)
@@ -29,22 +30,43 @@ module RbbtRESTHelpers
 
     step = Step.new(path, task, nil, nil, self)
 
+    halt 200, step.info.to_json if @format == :info
+
     self.instance_variable_set("@step", step)
 
     if @fragment
       fragment_file = step.file(@fragment)
       if File.exists?(fragment_file)
         case @format.to_s
-        when "tsv"
-          content_type "text/tab-separated-values"
-          send_file fragment_file
         when "table"
           halt 200, tsv2html(fragment_file)
         when "json"
-          halt 200, tsv_process(TSV.open(fragment_file)).to_json
+          halt 200, tsv_process(load_tsv(fragment_file).first).to_json
+        when "tsv"
+          content_type "text/tab-separated-values"
+          halt 200, tsv_process(load_tsv(fragment_file).first).to_s
+        when "entities"
+          tsv = tsv_process(load_tsv(fragment_file).first)
+          list = tsv.values.flatten
+          tsv.prepare_entity(list, tsv.fields.first, tsv.entity_options)
+          type = list.annotation_types.last
+          list_id = "List of #{type} in table #{ @fragment }"
+          list_id << " (#{ @filter })" if @filter
+          Entity::List.save_list(type.to_s, list_id, list, user)
+          header "Location", Entity::REST.entity_list_url(list_id, type)
+          redirect to(Entity::REST.entity_list_url(list_id, type))
+        when "map"
+          tsv = tsv_process(load_tsv(fragment_file).first)
+          type = tsv.keys.annotation_types.last
+          column = tsv.fields.first
+          map_id = "Map #{type}-#{column} in #{ @fragment }"
+          map_id << " (#{ @filter.gsub(';','|') })" if @filter
+          Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
+          url = Entity::REST.entity_map_url(map_id, type, column)
+          redirect to(url)
         when "excel"
           require 'rbbt/tsv/excel'
-          tsv = TSV.open(Open.open(fragment_file))
+          tsv = load_tsv(fragment_file).first
           content_type "text/html"
           data = nil
           excel_file = TmpFile.tmp_file
@@ -89,9 +111,12 @@ module RbbtRESTHelpers
     begin
       case step.status
       when :error, :aborted
-        error_for step, false
+        error_for step, !@ajax
       when :done
-        if send_file
+        case
+        when @permalink
+          redirect to(permalink(step.path))
+        when send_file
           send_file step.path
         else
           step.load

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

@@ -25,6 +25,39 @@ module RbbtRESTHelpers
     html_options = consume_parameter(:html_options, extra) || {}
 
     case type
+    when :multiple
+      choices = consume_parameter(:choices, extra)
+      default = default.collect{|o| o.to_s} if default
+      current = current.collect{|o| o.to_s} if current
+      input_label(id, name, description, Array === default ? default * ", " : nil, extra) +
+        choices.collect do |choice|
+          choice_name = name.to_s + "[#{ choice }]"
+        
+          check_true = (current && current.include?(choice.to_s)) || (default && default.include?(choice.to_s))
+
+          check_true = false if check_true.nil?
+            check_false = ! check_true
+            
+            choice_id = id + "[#{ Misc.snake_case(choice) }]"
+            if id
+              false_id = choice_id + '_false'
+              true_id  = choice_id + '_true'
+            else
+              false_id = nil
+              true_id = nil
+            end
+
+              #choice_html = html_tag("input", nil, :type => :hidden, :name => choice_name + "_checkbox_false", :value => "false") +
+              #  html_tag("input", nil, :type => :checkbox, :checked => check_true, :name => choice_name, :value => "true", :id => choice_id) +
+              #  input_label(choice_id, choice, nil, nil, extra.merge({:class => :inline})) 
+            
+              choice_html = html_tag("input", nil, :type => :checkbox, :checked => check_true, :name => choice_name, :value => "true", :id => choice_id) +
+                input_label(choice_id, choice, choice, nil, extra.merge({:class => :inline})) 
+
+              html_tag('span', choice_html, :class => 'choice')
+          end * "\n"
+
+
     when :boolean
       current = param2boolean(current) unless current.nil?
       default = param2boolean(default) unless default.nil?

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

@@ -26,6 +26,10 @@ module RbbtRESTHelpers
  
   #{{{ SASS
   
+  def self.add_sass_load_path(path)
+    Sass::Engine::DEFAULT_OPTIONS[:load_paths].unshift path
+  end
+ 
   def self.sass_resources
     @sass_resources ||= [Rbbt.share.views.compass.find(:lib)]
   end

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

@@ -5,6 +5,14 @@ module RbbtRESTHelpers
 
   PAGE_SIZE = 20
 
+  def log(status, message)
+    if @step
+      @step.log(status, message)
+    else
+      Log.debug("[#{ status }] #{ message }")
+    end
+  end
+
   def production?
     ENV["RACK_ENV"] == "production"
   end
@@ -41,6 +49,9 @@ module RbbtRESTHelpers
     @debug_js = consume_parameter(:_debug_js)
     @debug_js = false if @debug_js.nil? or @debug_js == "false"
 
+    @debug_css = consume_parameter(:_debug_css)
+    @debug_css = false if @debug_css.nil? or @debug_css == "false"
+
     @_ = consume_parameter(:_)
 
     @fragment = consume_parameter(:_fragment)
@@ -65,6 +76,8 @@ module RbbtRESTHelpers
       end
     end
 
+    @permalink = consume_parameter :_permalink
+
     @clean_params = params.dup
   end
  
@@ -91,6 +104,9 @@ module RbbtRESTHelpers
     when :float
       value.to_f
 
+    when :multiple
+      value.keys
+
     when :boolean
       param2boolean(value)
 
@@ -168,4 +184,12 @@ module RbbtRESTHelpers
     } * "\n"
     html_tag(:dl, entries, options)
   end
+
+  def permalink(path)
+    id = Misc.digest(Time.now.to_s)
+    dest = File.join(settings.permalink_dir, id)
+    FileUtils.mkdir_p settings.permalink_dir unless File.exists? settings.permalink_dir
+    FileUtils.ln_s(path, dest)
+    "/permalink/#{ id }"
+  end
 end

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

@@ -3,13 +3,17 @@ require 'rbbt/rest/common/cache'
 
 module RbbtRESTHelpers
   def error_for(job, layout = nil)
-    layout = @layout if layout.nil?
-    layout_file = (layout ? locate_template('layout') : nil)
-    template_file = locate_template('error')
+    if @format == :json
+      halt 400, {"message" => job.messages[-2], "backtrace" => job.info[:backtrace]}.to_json
+    else
+      layout = @layout if layout.nil?
+      layout_file = (layout ? locate_template('layout') : nil)
+      template_file = locate_template('error')
 
-    result = render template_file, {:job => job}, layout_file
+      result = render template_file, {:job => job}, layout_file
 
-    halt 500, result
+      halt 400, result
+    end
   end
 
   def wait_on(job, layout = nil)
@@ -29,16 +33,16 @@ module RbbtRESTHelpers
 
   def render(template_file, locals = {}, layout_file = nil, cache = nil, cache_options = {})
     if layout_file
-      Haml::Engine.new(Open.read(layout_file), :filename => layout_file).render(self) do
+      Haml::Engine.new(Open.read(layout_file), :filename => layout_file, :ugly => production?).render(self, locals) do
         cache(cache, locals.merge(:_template_file => template_file, :user => user).merge(cache_options)) do
           Log.debug("Rendering #{template_file} with layout")
-          Haml::Engine.new(Open.read(template_file), :filename => template_file).render(self, locals)
+          Haml::Engine.new(Open.read(template_file), :filename => template_file, :ugly => production?).render(self, locals)
         end
       end
     else
       cache(cache, locals.merge(:_template_file => template_file, :user => user).merge(cache_options)) do
         Log.debug("Rendering #{template_file} without layout")
-        Haml::Engine.new(Open.read(template_file), :filename => template_file).render(self, locals)
+        Haml::Engine.new(Open.read(template_file), :filename => template_file, :ugly => production?).render(self, locals)
       end
     end
   end
@@ -80,7 +84,7 @@ module RbbtRESTHelpers
         url = remove_GET_param(url, "_update")
         fragment_url = add_GET_param(url, "_fragment", fragment_code)
         if link.nil?
-          html_tag('a', " ", :href => fragment_url, :class => 'fragment')
+          html_tag('a', "", :href => fragment_url, :class => 'fragment')
         else
           if link =~ / href=/
             link.sub(/ href=('|")/," href='#{fragment_url}'")
@@ -143,5 +147,18 @@ module RbbtRESTHelpers
       raise "Type not understood: #{ type }"
     end
   end
+
+  def reveal(text, id = nil, &block)
+    id ||= "rbbt_reveal_" << (rand * 10000).to_i.to_s
+
+    content_html = capture_haml(&block)
+
+    str = html_tag('a', text.to_s, :href => "#", "data-reveal-id" => 'modal1', 'attr-reveal_id' => id, 'class' => 'rbbt_reveal_trigger') << 
+          "\n" <<
+          html_tag('div', "\n" << content_html << "\n", :id => id, 'class' => 'rbbt_reveal_content') << 
+          "\n"
+
+    str
+  end
 end
  

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

@@ -1,5 +1,4 @@
 require 'sass'
-#require 'yui/compressor'
 require 'uglifier'
 
 module RbbtRESTHelpers
@@ -22,6 +21,7 @@ module RbbtRESTHelpers
 
   def link_css(file)
     file += '.css' unless file =~ /.css$/
+    file << "?_update=reload" if @debug_css
     html_tag('link', nil, :rel => 'stylesheet', :type => 'text/css', :href => file)
   end
 

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

@@ -1,5 +1,24 @@
 require 'rbbt/entity'
 
+module Link
+  extend Entity
+
+  def self.tsv_sort(v)
+    value = v.last
+    value = value.first if Array === value
+    if value and value.match(/<a [^>]*>([^>]*)<\/a>/)
+      val = $1
+      if val =~ /^\s*\d/
+        val.to_f
+      else
+        val
+      end
+    else
+      ""
+    end
+  end
+end
+
 module NumericValue
   extend Entity
 
@@ -20,11 +39,17 @@ t.value
 t.values
 adjusted.p.value
 adjusted.p.values
+Rank
+rank
                 EOF
                ).split("\n")
 
   def <=>(other)
-    self.to_f <=> other.to_f
+    if Float === self
+      super(other.to_f)
+    else
+      self.to_f <=> other.to_f
+    end
   end
 
   def self.tsv_sort(v)
@@ -35,6 +60,10 @@ adjusted.p.values
       value.to_f
     end
   end
+
+  def to_s
+    "%.5g" % self.to_f
+  end
 end
 
 module RbbtRESTHelpers
@@ -44,13 +73,13 @@ module RbbtRESTHelpers
       tsv.collect{|id, value| [id, value]}
     when :list
       key_field = tsv.key_field
-      tsv.collect{|id, values| values = NamedArray.setup([id].concat(values), values.fields, id, values.entity_options, values.entity_templates); values.fields = [key_field].concat values.fields if values.respond_to? :fields; values }
+      tsv.collect{|id, values| new_values = [id].concat(values); begin NamedArray.setup(new_values, values.fields, id, values.entity_options, values.entity_templates); new_values.fields = [key_field].concat values.fields end if values.respond_to? :fields; new_values }
     when :flat
       key_field = tsv.key_field
       tsv.collect{|id, values| [id, values]}
     when :double
       key_field = tsv.key_field
-      tsv.collect{|id, value_lists|  value_lists = NamedArray.setup([id].concat(value_lists), value_lists.fields, id, value_lists.entity_options, value_lists.entity_templates); value_lists.fields = ([key_field].concat value_lists.fields) if value_lists.respond_to? :fields; value_lists }
+      tsv.collect{|id, value_lists| new_value_lists = [id].concat(value_lists); begin NamedArray.setup(new_value_lists, value_lists.fields, id, value_lists.entity_options, value_lists.entity_templates); new_value_lists.fields = ([key_field].concat value_lists.fields) end if value_lists.respond_to? :fields; new_value_lists }
     end
   end
 
@@ -78,7 +107,11 @@ module RbbtRESTHelpers
       reverse = false
     end
 
-    entity = Entity.formats[field]
+    if object.entity_templates[field]
+      entity = object.entity_templates[field].annotation_types.last
+    else
+      entity = Entity.formats[field] 
+    end
 
     num = num.to_i
     size = size.to_i
@@ -99,13 +132,13 @@ module RbbtRESTHelpers
     column = @column if column.nil?
 
     if filter and filter.to_s != "false"
-      filter.split("|").each do |f|
+      filter.split(";;").each do |f|
         key, value = f.split("~")
         case
         when value =~ /^([<>]=?)(.*)/
-          tsv = tsv.select(key){|k| k.send($1, $2)}
-        when value =~ /^\/.*\/$/
-          tsv = tsv.select(key => Regexp.new(value))
+          tsv = tsv.select(key){|k| k = k.first if Array === k; k.to_f.send($1, $2.to_f)}
+        when value =~ /^\/(.+)\/.{0,2}$/
+          tsv = tsv.select(key => Regexp.new($1))
         else
           tsv = tsv.select(key => value)
         end
@@ -119,26 +152,27 @@ module RbbtRESTHelpers
 
   def tsv_rows(tsv, page = nil, filter = nil, column = nil)
     tsv = tsv_process(tsv, filter, column)
+    length = tsv.size
     page = @page if page.nil?
     if page.nil? or page.to_s == "false"
-      tsv_rows_full(tsv)
+      [tsv_rows_full(tsv), length]
     else
-      tsv_rows_full(paginate(tsv, page))
+      [tsv_rows_full(paginate(tsv, page)), length]
     end
   end
 
 
   def table_value(value, type = nil, options = {})
     options = {} if options.nil?
-    return value.list_link :length, options[:list_id] if Array === value and options[:list_id] 
+    return value.list_link :length, options[:list_id] if Array === value and options[:list_id] and value.respond_to? :list_link
 
     entity_options = options[:entity_options]
 
-    Misc.prepare_entity(value, type, entity_options) if Entity.formats.include? type
+    Misc.prepare_entity(value, type, entity_options) if Entity.formats.include? type and not options[:unnamed]
 
     value = value.link if value.respond_to? :link
 
-    Array === value ? value * ", " : value
+    Array === value ? value.collect{|v| v.to_s} * ", " : value
   end
 
   def header(field, entity_type, entity_options = {})
@@ -151,12 +185,40 @@ module RbbtRESTHelpers
     @table_filters[field] = type
   end
 
+  def self.save_tsv(tsv, path)
+    Open.write(path, tsv.to_s)
+    table_options = {:tsv_entity_options => tsv.entity_options}
+    Open.write(path + '.table_options', table_options.to_yaml )
+  end
+
+  def self.load_tsv(file)
+    tsv = TSV.open(Open.open(file))
+
+    table_options = File.exists?(file + '.table_options') ? YAML.load_file(file + '.table_options') : {}
+    tsv.entity_options = table_options[:tsv_entity_options]
+    headers = table_options[:headers]
+    headers.each{|field,p| tsv.entity_templates[field] = Misc.prepare_entity("TEMPLATE", p.first, p.last) } unless headers.nil?
+
+    [tsv, table_options]
+  end
+
+  def save_tsv(file)
+    RbbtRESTHelpers.save_tsv(file)
+  end
+
+
+  def load_tsv(file)
+    RbbtRESTHelpers.load_tsv(file)
+  end
+
   def table(options = {})
     options = {} if options.nil?
 
     tsv = yield
 
-    table_code = (rand * 100000).to_i.to_s
+    table_code = options[:table_id] || (rand * 100000).to_i.to_s
+    table_code = Entity::REST.clean_element(table_code)
+    table_code.sub!(/[^\w]/,'_')
     table_file = @step.file(table_code)
 
     url = add_GET_param(@fullpath, "_fragment", File.basename(table_file))
@@ -191,20 +253,19 @@ module RbbtRESTHelpers
     tsv2html(table_file)
   end
 
-  def load_tsv(file)
-    tsv
-  end
-
-  def tsv2html(file)
-    tsv = TSV.open(Open.open(file))
 
-    table_options = File.exists?(file + '.table_options') ? YAML.load_file(file + '.table_options') : {}
-    tsv.entity_options = table_options[:tsv_entity_options]
-    headers = table_options[:headers]
-    filters = table_options[:filters]
-    headers.each{|field,p| tsv.entity_templates[field] = Misc.prepare_entity("TEMPLATE", p.first, p.last) } unless headers.nil?
+  def tsv2html(file, default_table_options = {})
+    if TSV === file
+      tsv, table_options = file, {}
+      table_options[:unnamed] = tsv.unnamed
+    else
+      tsv, table_options = load_tsv(file)
+    end
 
     content_type "text/html"
-    partial_render('partials/table', {:filters => filters, :total_size => tsv.size, :rows => tsv_rows(tsv), :header => tsv.all_fields, :table_options => table_options})
+    rows, length = tsv_rows(tsv)
+
+    table_options = default_table_options.merge(table_options)
+    partial_render('partials/table', {:total_size => length, :rows => rows, :header => tsv.all_fields, :table_options => table_options})
   end
 end