rbbt-rest 1.9.1 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f704f277ce12001953704f8e901241c79f1bc0d6425967ae231455671bfa7879
-  data.tar.gz: 07d4ca572f44e36384bd7595f1c36738b6388c4f3da1fa03827a118b5eed3724
+  metadata.gz: ee4b57a3f56a52f3fee6a0a1b8827835d7b0c8d45376be1f666faf4501451560
+  data.tar.gz: f703d52fc992dc38937859074ee046d06ac6028b596536f8ec4ebddcf5445144
 SHA512:
-  metadata.gz: ca607c13addb28475b071f500a50e9ccac7c13007e765fb044cba6e9f41735a45e0de2ad403984bbaaf36ba662397140f06d542090bb9936981890d4b5b988c5
-  data.tar.gz: d2f72803da7071b5e0d2c743344dc120e7ad56c387ada1d002492ad5b0eeab138b5cd0d630b72af9e5fe8156268d36f65288193c494e2c2ced69c9e6829288b6
+  metadata.gz: cd74b954053885e3eb8fa97d3c160cc3d4c148dc18f4f013489d296dc07cad2ca93b577e8119fc82240ea7ad5e49ed60545460a7684ebe592cb1a1567a72d6eb
+  data.tar.gz: 1ed08a5a7b9ecd465acb27e4cedff76affdb581980449883c2540f3ff941ee4bfdcfdc0a3c621d66e6f283d9bcecedfe046478f0423f995fcac40d29d55e45fe

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

@@ -50,17 +50,22 @@ module RbbtRESTHelpers
              params[:cache_file] 
            else
              if post_hash = params["__post_hash_id"]
-               name = name.gsub("/",'>') << "_" << post_hash
+               name = name.gsub("/",'·') << "_" << post_hash
              elsif params
                param_hash = Misc.obj2digest(params)
-               name = name.gsub("/",'>') << "_" << param_hash 
+               name = name.gsub("/",'·') << "_" << param_hash 
              end
              settings.cache_dir[name].find
            end
 
     task = Task.setup(:name => orig_name, :result_type => :string, &block)
 
-    step = Step.new(path, task, nil, nil, self)
+    if defined?(Scout)
+      step = Step.new(path, nil, nil, self, &task)
+      step.exec_context = self
+    else
+      step = Step.new(path, task, nil, nil, self)
+    end
 
     halt 200, step.info.to_json if @format == :info
 
@@ -103,7 +108,9 @@ module RbbtRESTHelpers
     #step.instance_variable_set(:@url_path, URI(clean_url).path)
     step.instance_variable_set(:@url, clean_url)
     step.instance_variable_set(:@url_path, URI(clean_url).path)
-    step.clean if step.error? || step.aborted?
+    if (step.error? && step.recoverable_error?) || step.aborted?
+      step.clean 
+    end
 
     Thread.current["step_path"] = step.path
     # Issue
@@ -170,7 +177,7 @@ module RbbtRESTHelpers
           tsv = tsv_process(raw_tsv)
 
           list = tsv.values.flatten
-          tsv.prepare_entity(list, tsv.fields.first, tsv.entity_options)
+          list = 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
@@ -306,6 +313,7 @@ data = NULL
     begin
 
       if step.done?
+        step.join
         case
         when @permalink
           redirect to(permalink(step.path))

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

@@ -10,7 +10,8 @@ module RbbtRESTHelpers
   def add_search_paths(path, resources)
     resources.reverse.each do |resource|
       name = Misc.snake_case(resource.to_s.gsub('/','_'))
-      path.prepend_search_path(name, resource)
+      #path.prepend_search_path(name, resource)
+      path.prepend_path(name, resource)
     end
   end
 
@@ -38,11 +39,11 @@ module RbbtRESTHelpers
   #{{{ TEMPLATE
   
   def self.template_resources
-    @template_resources ||= [Rbbt.share.views.find(:lib)]
+    @@template_resources ||= [Rbbt.share.views.find(:lib)]
   end
 
   def template_resources
-   [Rbbt.www.views] + RbbtRESTHelpers.template_resources
+    [Rbbt.www.views] + RbbtRESTHelpers.template_resources
   end
 
   def locate_template(template)

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

@@ -4,6 +4,11 @@ require 'haml'
 module RbbtRESTHelpers
   class Retry < Exception; end
 
+  def persist(name, type = :marshal, options = {}, &block)
+    options[:dir] = settings.cache_dir.find
+    Persist.persist(name, type, options, &block)
+  end
+
   def check_step(step)
     if File.exist?(step.info_file) and Time.now - File.atime(step.info_file) > 60
       done = step.done?
@@ -57,7 +62,12 @@ module RbbtRESTHelpers
   end
 
   def process_common_parameters
+    process_request_and_params(request, params)
+  end
+
+  def process_request_and_params(request, params)
     @ajax = request.xhr?
+    @params = params
 
     @uri = request.env["REQUEST_URI"]
     @uri = remove_GET_param(@uri, ["_update", "_", "_layout"])
@@ -66,12 +76,12 @@ module RbbtRESTHelpers
 
     @uri = post_uri if @is_method_post
 
-    @path = request.env["PATH_INFO"]
+    @path_info = request.env["PATH_INFO"]
     @query = request.env["QUERY_STRING"]
-    @fullpath = (@query && ! @query.empty?) ? @path + "?" + @query : @path
+    @fullpath = (@query && ! @query.empty?) ? @path_info + "?" + @query : @path_info
     @fullpath = remove_GET_param(@fullpath, ["_update", "_", "_layout"])
 
-    @ajax_url = @uri
+    @ajax_url = @fullpath
 
     @layout = consume_parameter(:_layout)
 
@@ -143,7 +153,7 @@ module RbbtRESTHelpers
   end
  
   def consume_parameter(parameter, params = nil)
-    params = self.params if params.nil?
+    params = @params ||= self.params if params.nil?
 
     val = params.delete(parameter.to_sym) 
     val = params.delete(parameter.to_s) if val.nil?
@@ -274,10 +284,14 @@ module RbbtRESTHelpers
       param.each do |p|
         url = remove_GET_param(url, p)
       end
-      url
     else
-      url.gsub(/&?#{param}=[^&]+/,'').sub(/\?$/, '')
+      url = url.gsub(/(\?|&)#{param}=[^&]+/,'\1')
     end
+
+    url = url.sub(/&$/, '')
+    url = url.sub(/\?$/,'')
+
+    url
   end
 
   def add_GET_param(url, param, value)
@@ -320,6 +334,22 @@ module RbbtRESTHelpers
     halt response, html
   end
 
+  def capture(*args, &block)
+
+    variables = block.binding.local_variables
+    buff_var = variables.select{|v| v.to_s =~ /^_module\d+$/}.sort_by{|v| v.to_s.scan(/\d+/).first.to_i}.last
+    buff_was = block.binding.local_variable_get(buff_var) if variables.include? buff_var
+    block.binding.local_variable_set(buff_var,'') if buff_var
+    begin
+      raw = block.call(*args)
+      captured = block.binding.local_variable_get(buff_var) if block.binding.local_variables.include?(buff_var)
+      captured = "" if captured.nil?
+      captured = raw if captured.empty? 
+      captured
+    ensure
+      block.binding.local_variable_set(buff_var, buff_was) if buff_was
+    end
+  end
 end
 
 if $haml_6

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

@@ -6,9 +6,15 @@ Tilt::SYMBOL_ARRAY_SORTABLE = false
 module RbbtRESTHelpers
   def error_for(job, layout = nil)
     if ex = job.info[:exception]
-      klass = ex[:class]
-      msg = ex[:message]
-      bkt = ex[:backtrace]
+      if Exception === ex
+        klass = ex.class
+        msg = ex.message
+        bkt = ex.backtrace
+      else
+        klass = ex[:class]
+        msg = ex[:message]
+        bkt = ex[:backtrace]
+      end
     elsif job.dirty?
       klass = "Exception"
       msg = "Job dirty"
@@ -232,7 +238,7 @@ module RbbtRESTHelpers
     filename = Misc.sanitize_filename(Misc.name2basename(filename))
 
     if @step
-      url = add_GET_param(remove_GET_param(@uri, ["_update", "_"]), "_fragment", "html_resources/#{ filename }")
+      url = add_GET_param(remove_GET_param(@fullpath, ["_update", "_"]), "_fragment", "html_resources/#{ filename }")
       f = @step.file(:html_resources)[filename].find
     else
       url = "/files/#{ filename }"
@@ -249,7 +255,7 @@ module RbbtRESTHelpers
     when :image
       "<img src='#{url}' alt='#{text}' class='file_resource'/>"
     when :link
-      "<a href='#{url}' class='file_resource'>#{ text }</a>"
+      "<a href='#{url}' class='file_resource' download='#{filename}'>#{ text }</a>"
     when :linked_image
       "<a href='#{url}' class='file_resource' target='_blank'><img src='#{url}' class='file_resource'/></a>"
     when :zoomable_image
@@ -270,7 +276,7 @@ module RbbtRESTHelpers
     filename = File.basename(TmpFile.tmp_file) if filename.nil?
 
     if @step
-      url = add_GET_param(remove_GET_param(@uri, ["_update", "_"]), "_fragment", "json_resources/#{ filename }")
+      url = add_GET_param(remove_GET_param(@fullpath, ["_update", "_"]), "_fragment", "json_resources/#{ filename }")
       f = @step.file(:json_resources)[filename].find
     else
       url = "/files/#{ filename }"

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

@@ -77,6 +77,12 @@ module NumericValue
   extend Entity
 
   self.format =(<<-EOF
+NumericValue
+Numeric Value
+Numeric
+numeric_value
+numeric value
+numeric
 p-value
 p-value
 p.value
@@ -147,44 +153,19 @@ end
 
 module RbbtRESTHelpers
 
-  def capture(*args, &block)
-
-    variables = block.binding.local_variables
-    #variables.each do |v|
-    #  iif [v, block.binding.local_variable_get(v)]
-    #end
-    buff_var = variables.select{|v| v.to_s =~ /^_module\d+$/}.sort_by{|v| v.to_s.scan(/\d+/).first.to_i}.last
-    buff_was = block.binding.local_variable_get(buff_var) if variables.include? buff_var
-    block.binding.local_variable_set(buff_var,'') if buff_var
-    begin
-      raw = block.call(*args)
-      #variables = block.binding.local_variables
-      #iii variables
-      #variables.each do |v|
-      #  iif [v, block.binding.local_variable_get(v)]
-      #end
-      captured = block.binding.local_variable_get(buff_var) if block.binding.local_variables.include?(buff_var)
-      captured = "" if captured.nil?
-      captured = raw if captured.empty? 
-      captured
-    ensure
-      block.binding.local_variable_set(buff_var, buff_was) if buff_was
-    end
-  end
-  
   def tsv_rows_full(tsv)
     case tsv.type 
     when :single
       tsv.collect{|id, value| [id, value]}
     when :list
       key_field = tsv.key_field
-      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 }
+      tsv.collect{|id, values| new_values = [id].concat(values); begin NamedArray.setup(new_values, values.fields, id, values.entity_options); 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| 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 }
+      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); new_value_lists.fields = ([key_field].concat value_lists.fields) end if value_lists.respond_to? :fields; new_value_lists }
     end
   end
 
@@ -195,6 +176,7 @@ module RbbtRESTHelpers
 
     field = "key" if field.nil? or field.empty?
     size = PAGE_SIZE if size.nil? or size.empty?
+    num = 1 if num.nil? || num.empty?
 
     [num, size, field]
   end
@@ -214,11 +196,7 @@ module RbbtRESTHelpers
 
     field =  CGI.unescapeHTML(Entity::REST.restore_element(field))
 
-    if object.entity_templates[field]
-      entity = object.entity_templates[field].annotation_types.last
-    else
-      entity = Entity.formats[field] 
-    end
+    entity = Entity.formats[field] 
 
     if num == 'all'
       num = 1
@@ -235,9 +213,9 @@ module RbbtRESTHelpers
 
     object.with_unnamed do
       if entity and entity.respond_to? :tsv_sort
-        object.page(num, size, field, false, reverse, &entity.method(:tsv_sort))
+        object.page(num, size, field, false, reverse, &entity.method(:tsv_sort)).tap{|o| o.unnamed = false }
       else
-        object.page(num, size, field, false, reverse)
+        object.page(num, size, field, false, reverse).tap{|o| o.unnamed = false }
       end
     end
   end
@@ -389,19 +367,7 @@ module RbbtRESTHelpers
 
   def self.save_tsv(tsv, path)
     Open.write(path, tsv.to_s)
-    table_options = {:tsv_entity_options => tsv.entity_options, :tsv_entity_templates => tsv.entity_templates}
-    if tsv.entity_templates and tsv.entity_templates.any?
-      table_options[:headers] ||= {}
-      tsv.entity_templates.each do |field,template|
-        next if template.nil?
-        next if table_options[:headers].include? field
-        info = template.info
-        info.delete :format
-        info.delete :annotation_types
-        info.delete :annotated_array
-        table_options[:headers][field] = [template.annotation_types.last.to_s, info]
-      end
-    end
+    table_options = {:tsv_entity_options => tsv.entity_options}
     Open.write(path + '.table_options', table_options.to_yaml )
   end
   
@@ -442,7 +408,7 @@ module RbbtRESTHelpers
     if @step
       table_file = @step.file(table_code) if @step
 
-      url = add_GET_param(@uri, "_fragment", File.basename(table_file))
+      url = add_GET_param(@fullpath, "_fragment", File.basename(table_file))
       url = remove_GET_param(url, "_update")
       url = remove_GET_param(url, "_layout")
       url = remove_GET_param(url, "_")

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

@@ -63,7 +63,7 @@ module EntityRESTHelpers
     locals = {}
     info = {:inputs => inputs, :input_descriptions => input_descriptions, :input_defaults => input_defaults, :input_options => input_options, :input_types => input_types, :values => values}
     locals[:id] = action_parameters_id
-    locals[:action] = @ajax_url
+    locals[:action] = @fullpath
     locals[:klass] = 'action_parameter_form'
     locals[:info] = info
     #locals[:description] = description

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

@@ -223,11 +223,8 @@ module EntityRESTHelpers
 
     field = map.key_field
 
-    if map.entity_templates[field] 
-      types = map.entity_templates[field].annotation_types
-    else
-      types = [Entity.formats[field]].compact
-    end
+    types = [Entity.formats[field]].compact
+
     types += ["Default"]
 
     path = nil
@@ -248,11 +245,8 @@ module EntityRESTHelpers
 
     field = map.key_field
 
-    if map.entity_templates[field] 
-      types = map.entity_templates[field].annotation_types
-    else
-      types = [Entity.formats[field]].compact
-    end
+    types = [Entity.formats[field]].compact
+
     types += ["Default"]
 
     paths = types.inject([]) do |acc,type|

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

@@ -28,8 +28,7 @@ module EntityRESTHelpers
       entity_annotations[annotation] = value
     end
 
-    entity.extend entity_class
-    entity_class.setup_hash(entity, entity_annotations)
+    entity_class.setup(entity, entity_annotations)
     entity.format = format if format and entity.respond_to? :format
 
     entity

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

@@ -122,7 +122,6 @@ module Entity
     #{{{ LINKS
 
     def link(text = nil, options = {})
-      #return self.tap{|a| a.extend AnnotatedArray}.collect{|e| e.link(text, options) } if Array === self
       return self.collect{|e| e.nil? ? nil : e.link(text, options) } if Array === self
       return self.split(";").collect{|e| self.annotate(e).link(text, options) } * ", " if self.include? ";"
       return nil if self.empty?
@@ -187,7 +186,7 @@ module Entity
 
       reuse = options.delete(:reuse)
       reuse = options.delete("reuse") if reuse.nil?
-      reuse = true if reuse.nil?
+      reuse = false if reuse.nil?
 
       Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exist?(Entity::List.list_file(entity_type.to_s, id))
 

data/lib/rbbt/rest/entity.rb

@@ -201,8 +201,10 @@ module Sinatra
 
           annotations[:annotation_types] ||= [type]
 
+          annotations.delete_if{|k,v| v.empty? }
+
           mod = Kernel.const_get(type)
-          list = mod.setup(entities.reject{|e| e.empty?}, annotations)
+          list = mod.setup(entities.reject{|e| e.empty? }, annotations)
 
           Entity::List.save_list(type, list_id, list, user)
 

data/lib/rbbt/rest/main.rb

@@ -18,6 +18,7 @@ require 'nakayoshi_fork'
 
 Rbbt.add_version(__FILE__)
 
+Path.add_path :rbbt_rest, File.join(Path.caller_lib_dir(__FILE__), "{TOPLEVEL}/{SUBPATH}")
 module Sinatra
   module RbbtRESTMain
 
@@ -133,7 +134,7 @@ module Sinatra
             Log.info{ "Profile saved at #{ dir }: #{@uri}" }
           end
 
-          response.header["URI"] = @uri
+          headers "URI" => @uri
         end
 
         add_sass_load_path Rbbt.views.compass.find

data/lib/rbbt/rest/workflow/jobs.rb

@@ -269,7 +269,7 @@ module WorkflowRESTHelpers
 
       begin
         # $rest_cache_semaphore is defined in rbbt-util etc/app.d/semaphores.rb
-        job.fork($rest_cache_semaphore) unless job.started?
+        job.fork(true, $rest_cache_semaphore) unless job.started?
 
         if @format == :jobname
           job.soft_grace
@@ -311,7 +311,11 @@ module WorkflowRESTHelpers
   end
 
   def abort_job(workflow, job)
-    job.abort
+    begin
+      job.abort
+    rescue Exception
+      Log.exception $!
+    end
     halt 200, "Aborted #{ job.path }"
   end
 

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

@@ -6,7 +6,7 @@ module WorkflowRESTHelpers
   end
 
   def workflow_resources
-    [Rbbt.www.views.find(:lib)] + WorkflowRESTHelpers.workflow_resources
+    @workflow_resources ||= [Rbbt.www.views.find(:lib)] + WorkflowRESTHelpers.workflow_resources
   end
 
   def locate_workflow_template(template, workflow = nil, task = nil)

data/lib/rbbt/rest/workflow.rb

@@ -235,7 +235,7 @@ module Sinatra
           task_inputs = task_info[:inputs]
           TmpFile.with_file do |basedir|
             dir = File.join(basedir, 'inputs')
-            Step.save_job_inputs(job, dir)
+            workflow.tasks[task].save_inputs(dir, job.recursive_inputs)
             filename = File.join(basedir, job.clean_name + '.input_bundle.tar.gz')
             content_type "application/tar+gzip"
             Misc.consume_stream(Misc.tarize(dir), false, filename)
@@ -317,6 +317,7 @@ module Sinatra
         #  end
         #end
         mime = file_mimetype(path)
+        mime = 'html' if path.ends_with?('.html')
         content_type mime if mime
         send_file path
       end

data/share/views/entity_partials/action_controller.haml

@@ -25,7 +25,7 @@
         - controller.actions.each do |action, text, resource, params|
           -#.ui.item.button(class="#{last_resource and last_resource != resource ? "new_resource" : ""}" attr-resource="#{resource}")
           - case
-          - when AnnotatedArray === entity
+          - when (AnnotatedArray === entity) && (Array === entity)
             - id = params.delete :id if Hash === params
             - id = controller.id if id.nil?
             = entity.list_action_link action, text, id, params.merge(:reuse => true, :class => 'ui item button')

data/share/views/entity_partials/entity_card.haml

@@ -96,7 +96,7 @@
       - if defined? block and block
         /-- description block --
         .description.ui.basic.segment<
-          = capture &block
+          = capture(&block)
 
       - card.sections.each do |name,section_block|
         .ui.very.basic.segment(id="#{Misc.snake_case(name)}")

data/share/views/entity_partials/entity_map_card.haml

@@ -83,7 +83,7 @@
     .content
       .description
         = table :class => 'ui collapsing table', :table_id => map_id do
-          - map
+          - next map
       - if card.action_controller
         .actions
           = action_controller_render(card.action_controller)

data/share/views/error.haml

@@ -13,30 +13,31 @@
     - else
       - if ! job.updated?
         %pre.error_message.ui.basic.segment.content
-          Job out of date. Dependencies: #{job.out_of_date.collect{|d| d.path} * ", "}
+          Job out of date. Dependencies: #{job.newer_dependencies.collect{|d| d.path} * ", "}
       - else
         %pre.error_message.ui.basic.segment.content
           Unknown Error (status: #{job.status})
     
 
 
-  - if defined? job.info_file and Open.exists? job.info_file and @uri.include? job.name
-    - clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "clean")
+  - if defined? job.info_file and Open.exists? job.info_file and @path_info.include? job.name
+    - clean_url = add_GET_param(remove_GET_param(@path_info, "_layout"), "_update", "clean")
     %a.ui.button.blue.clean(href=clean_url) Clean
   - else
-    - clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "reload")
+    - clean_url = add_GET_param(remove_GET_param(@path_info, "_layout"), "_update", "reload")
     %a.ui.blue.button.reload(href=clean_url) Reload
 
-  - info_url = @uri.sub(/\?.*/,'') + '/info'
-  - if @uri.include? job.name
+  - info_url = @path_info.sub(/\?.*/,'') + '/info'
+  - if @path_info.include? job.name
     %a.ui.blue.button.reload(href=info_url) Info
 
-  - if job.files.any? and @uri.include? job.name
-    - files_url = @uri.sub(/\?.*/,'') + '/files'
+  - if job.files.any? and @path_info.include? job.name
+    - files_url = @path_info.sub(/\?.*/,'') + '/files'
     %a.ui.blue.button.reload(href=files_url) Files
 
 
 - backtrace = job.info[:backtrace]
+- backtrace ||= job.info[:exception].backtrace if Exception === job.info[:exception]
 - if backtrace and backtrace.any?
 
   .error_backtrace.clean_list.ui.segment

data/share/views/job_info.haml

@@ -49,7 +49,8 @@
               overflow: auto
               border: 1px solid #EEE
 
-          - inputs.fields.each_with_index do |f, ix|
+          - input_fields = Hash === inputs ? inputs.keys : inputs.fields
+          - input_fields.each_with_index do |f, ix|
             - i = inputs[ix]
             - next unless task_inputs.include?(f)
             %dt= f
@@ -73,7 +74,7 @@
   - if exception
     - tab.active "Exception"
     - tab.add "Exception" do
-      - backtrace = exception[:backtrace]
+      - backtrace = exception.respond_to?(:backtrace) ? exception.backtrace : exception[:backtrace]
       .error_backtrace.clean_list
         .ui.header Backtrace
         %pre.ui.content

data/share/views/job_result/text.haml

@@ -1,4 +1,6 @@
 - if job.path =~ /\.svg$/i
   = result
 - else
-  %pre.result_text= result
+  %pre.result_text
+    :escaped 
+      #{result}

data/share/views/job_result.haml

@@ -2,7 +2,7 @@
   .job_control
     = workflow_partial('job_result/job_control', workflow, task, locals)
 
-- type ||= job.info[:result_type]
+- type ||= job.info[:result_type] || job.info[:type]
 - case type
 - when :tsv
   = workflow_partial('job_result/tsv', workflow, task, locals)

data/share/views/layout/top_menu.haml

@@ -11,18 +11,32 @@
         %input(type="search" name="term" placeholder='Search')
 
   #aesthetics.item
+  - main_actions = glob_all_server_files("main/*.haml", RbbtRESTHelpers.template_resources)
+  - if main_actions.any?
+    - main_actions = main_actions.collect do |file|
+      - _, _, filename = file.partition("main/")
+      - filename.sub('.haml','')
+    .main.ui.simple.dropdown.item.right
+      %i.icon.dropdown
+      Main pages
+      .menu
+        - main_actions.each do |action|
+          %a.item(href='#{'/main/' + action}')
+            = action.to_s
+      
+
   - if defined? Sinatra::RbbtRESTWorkflow and Sinatra::RbbtRESTWorkflow::WORKFLOWS
-    - expoted_workflows = Sinatra::RbbtRESTWorkflow::WORKFLOWS.collect do |workflow|
+    - exported_workflows = Sinatra::RbbtRESTWorkflow::WORKFLOWS.collect do |workflow|
       - next if workflow.asynchronous_exports.empty? and workflow.synchronous_exports.empty? and workflow.exec_exports.empty?
       - workflow
 
-    - expoted_workflows.compact!
-    - if expoted_workflows.any?
+    - exported_workflows.compact!
+    - if exported_workflows.any?
       .workflow.ui.simple.dropdown.item.right
         %i.icon.dropdown
         Workflows
         .menu
-          - expoted_workflows.each do |workflow|
+          - exported_workflows.each do |workflow|
             %a.item(href='#{'/' + workflow.to_s}')
               - if production?
                 = workflow.to_s

data/share/views/partials/dependencies.haml

@@ -1,88 +1,89 @@
 
 - cache = {} if not defined?(cache) or cache.nil?
 
-%ul.dependencies
-  - job.dependencies.reverse.each do |dep|
-    - dep_workflow = dep.workflow 
-    - dep_workflow = nil if dep_workflow == ""
-    - dep_workflow ||= dep.task.workflow if dep.task
-    - dep_workflow = nil if dep_workflow == ""
-    - dep_workflow ||= File.basename(File.dirname(File.dirname(dep.path)))
-    - dep_workflow = nil if dep_workflow == ""
-    - str = [dep_workflow, dep.task_name, dep.name].compact * " - "
-    - remote = true if Open.remote?(dep.path) || Open.ssh?(dep.path)
+- if job.dependencies
+  %ul.dependencies
+    - job.dependencies.reverse.each do |dep|
+      - dep_workflow = dep.workflow 
+      - dep_workflow = nil if dep_workflow == ""
+      - dep_workflow ||= dep.task.workflow if dep.task
+      - dep_workflow = nil if dep_workflow == ""
+      - dep_workflow ||= File.basename(File.dirname(File.dirname(dep.path)))
+      - dep_workflow = nil if dep_workflow == ""
+      - str = [dep_workflow, dep.task_name, dep.name].compact * " - "
+      - remote = true if Open.remote?(dep.path) || Open.ssh?(dep.path)
 
-    - if remote
-      - dep_status = "done" if dep.done?
-    - else
-      - dep_status = "done" if dep.path.exists?
+      - if remote
+        - dep_status = "done" if dep.done?
+      - else
+        - dep_status = "done" if Open.exists?(dep.path)
 
-    - dep_status ||= dep.status
-    - if ! remote && ! dep_status == 'done' && dep.file(:progress).exists?
-      - pgr = dep.file(:progress).yaml
-      - if pgr and pgr[:last_percent]
-        - start = pgr[:start]
-        - last_time = pgr[:last_time]
+      - dep_status ||= dep.status
+      - if ! remote && ! dep_status == 'done' && dep.file(:progress).exists?
+        - pgr = dep.file(:progress).yaml
+        - if pgr and pgr[:last_percent]
+          - start = pgr[:start]
+          - last_time = pgr[:last_time]
 
-        - ellapsed = last_time - start
-        - if pgr[:mean]
-          - missing = pgr[:max].to_f - pgr[:ticks].to_f
-          - eta = missing / pgr[:mean].to_f
-        - else
-          - ratio = pgr[:ticks].to_f/pgr[:max].to_f
-          - eta = ellapsed * (1 - ratio)
-        - eta = Misc.format_seconds(eta)
-        - ellapsed = Misc.format_seconds(ellapsed)
-        - pgr_str = " - " + pgr[:last_percent].to_s + "%" + " " + eta
+          - ellapsed = last_time - start
+          - if pgr[:mean]
+            - missing = pgr[:max].to_f - pgr[:ticks].to_f
+            - eta = missing / pgr[:mean].to_f
+          - else
+            - ratio = pgr[:ticks].to_f/pgr[:max].to_f
+            - eta = ellapsed * (1 - ratio)
+          - eta = Misc.format_seconds(eta)
+          - ellapsed = Misc.format_seconds(ellapsed)
+          - pgr_str = " - " + pgr[:last_percent].to_s + "%" + " " + eta
 
-        :deferjs
-          var percent = '#{pgr[:last_percent]}';
-          var task = '#{dep.task_name}';
-          var title = $('head title');
-          var current = title.text();
-          var newtext;
-          var pos = current.indexOf('%');
-          if (pos == -1){
-            newtext = task + " - " + percent + "% " + current
-          }else{
-            newtext = task + " - " + percent + "% " + current.slice(pos+1)
-          }
-          title.text(newtext)
+          :deferjs
+            var percent = '#{pgr[:last_percent]}';
+            var task = '#{dep.task_name}';
+            var title = $('head title');
+            var current = title.text();
+            var newtext;
+            var pos = current.indexOf('%');
+            if (pos == -1){
+              newtext = task + " - " + percent + "% " + current
+            }else{
+              newtext = task + " - " + percent + "% " + current.slice(pos+1)
+            }
+            title.text(newtext)
 
+        - else
+          - pgr_str = " - " + pgr[:ticks].to_s 
+        - status = dep_status.to_s + pgr_str
       - else
-        - pgr_str = " - " + pgr[:ticks].to_s 
-      - status = dep_status.to_s + pgr_str
-    - else
-      - status = dep_status
-    - name = dep.name
-    %li
-      %span.workflow= dep_workflow
-      %span.task= dep.task_name
-      %span.name
-        - if String === dep_workflow
-          - wf ||= begin
-            - Kernel.const_get dep_workflow
-            - rescue
-        - elsif Module === dep_workflow
-          - wf = dep_workflow
+        - status = dep_status
+      - name = dep.name
+      %li
+        %span.workflow= dep_workflow
+        %span.task= dep.task_name
+        %span.name
+          - if String === dep_workflow
+            - wf ||= begin
+              - Kernel.const_get dep_workflow
+              - rescue
+          - elsif Module === dep_workflow
+            - wf = dep_workflow
 
-        - if remote
-          - url = dep.path.split("?").first
-          %a(href=url) #{ name }  
+          - if remote
+            - url = dep.path.split("?").first
+            %a(href=url) #{ name }  
 
-        - elsif wf and Sinatra::RbbtRESTWorkflow::WORKFLOWS.include?(wf) and wf.task_exports.include? dep.task_name.to_sym
-          - url = "/" + [dep_workflow.to_s, dep.task_name.to_s, dep.name.to_s] * "/"
-          %a(href=url) #{ name }  
+          - elsif wf and Sinatra::RbbtRESTWorkflow::WORKFLOWS.include?(wf) and wf.task_exports.include? dep.task_name.to_sym
+            - url = "/" + [dep_workflow.to_s, dep.task_name.to_s, dep.name.to_s] * "/"
+            %a(href=url) #{ name }  
 
-        - else
-          = name 
+          - else
+            = name 
 
 
-      %span.status(class="#{dep_status}") [#{status}]
+        %span.status(class="#{dep_status}") [#{status}]
 
-      - if dep.dependencies && dep.dependencies.any?
-        - if cache[dep.path]
-          = reveal "(deps)", nil, :title => "Dependencies already shown above", "attr-reveal_title" => "#{[dep_workflow, dep.task_name, dep.name] * " # "}"  do
-            = cache[dep.path]
-        - else
-          = cache[dep.path] ||= partial_render('partials/dependencies', :job => dep, :cache => cache)
+        - if dep.dependencies && dep.dependencies.any?
+          - if cache[dep.path]
+            = reveal "(deps)", nil, :title => "Dependencies already shown above", "attr-reveal_title" => "#{[dep_workflow, dep.task_name, dep.name] * " # "}"  do
+              = cache[dep.path]
+          - else
+            = cache[dep.path] ||= partial_render('partials/dependencies', :job => dep, :cache => cache)

data/share/views/partials/form.haml

@@ -60,7 +60,7 @@
     - if uses
       - uses.each do |workflow, tasks|
         - tasks.each do |task|
-          - use_tags << [workflow, task] * "#"
+          - use_tags << [workflow.to_s, task.to_s] * "#"
     - input_id = id.nil? ? nil : id + "__" << input.to_s
     - hide = (options[input] != nil and options[input][:hide])
     %div(class="field #{types[input]} #{input} #{hide ? 'hide' : ''}" attr-use_tags='#{use_tags * " "}')
@@ -72,7 +72,8 @@
         - uses.each do |workflow, tasks|
           - tasks.each do |task|
             - description << " * " << [workflow.to_s, task] * "#" << "\n"
-      !~ form_input(input, types[input], defaults[input], values[input] || locals[input], description, input_id, input_options)
+      - value = values[input].nil? ? locals[input] : values[input]
+      !~ form_input(input, types[input], defaults[input], value, description, input_id, input_options)
 
 
   - if bundle && inputs.any?

data/share/views/partials/table.haml

@@ -50,8 +50,13 @@
 
       %tr(id=row_id)
         - row.each_with_index do |value, i|
-          - list_id = "#{ Misc.humanize(table_id) }: #{header[i]} for #{row.first}" if list_links and table_id and header and AnnotatedArray === value
           - field = header ? header[i] : nil
+          - if entity_headers && entity_headers[field]
+            - entity_field, entity_options = entity_headers[field]
+            - value = Entity.prepare_entity(value, entity_field, entity_options)
+          - else
+            - value = Entity.prepare_entity(value, field)
+          - list_id = "#{ Misc.humanize(table_id) }: #{header[i]} for #{row.first}" if list_links and table_id and header and AnnotatedArray === value
           - val = table_value(value, field, :list_id => list_id, :unnamed => unnamed, :entity_options => entity_options, :span => span)
           - case val.to_s
           - when 'TRUE', 'true', 'Yes', 'yes'

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

@@ -130,7 +130,7 @@ body.on('click', '.edit_list input[type=submit]', function(){
 
   if (undefined !== format){ entity_type = entity_type + ':' + clean_element(format) }
 
-  var url = '/entity_list/' + clean_element(entity_type) + '/' + clean_element(new_list_id  )
+  var url = '/entity_list/' + clean_element(entity_type) + '/' + clean_element(new_list_id)
 
   url = rbbt.url_add_script_name(url)
   get_ajax({url: url, type: 'POST', async: false, data: {annotations: JSON.stringify(annotations), entities: entities}}, function(){ window.location = url })

data/share/views/tasks.haml

@@ -20,9 +20,7 @@
 
     - tasks.sort.each do |task|
       %li
-        //%a(href="#{to(File.join("/", workflow.to_s, task.to_s))}")= task
         %a(href="#{File.join("/", workflow.to_s, task.to_s)}")= task
-        - info = workflow.task_info(task)
-        - if info[:description]
-          %span= info[:description].split(/\n\s*\n/).first
+        - if workflow.tasks[task].description
+          %span= workflow.tasks[task].description.split(/\n\s*\n/).first
 

data/share/views/tools/Rggplot.haml

@@ -4,12 +4,16 @@
 - size = 3 unless defined? size and size
 - width = size unless defined? width and width
 - height = size unless defined? height and height
+- svg = true unless defined? svg
 - plot = block.call unless (defined? plot and plot) or not defined? block
 - plot_options = {} unless defined? plot_options and plot_options
 
 - filename += '.png' unless filename =~ /\.png$/i
 - require 'rbbt/util/R'
 
-= resource filename, text, :image do |filename|
-  - R::PNG.ggplot(filename, data, plot, width, height, plot_options) 
+- if svg
+  = R::SVG.ggplot(data, plot, width, height, plot_options) 
+- else
+  = resource filename, text, :image do |filename|
+    - R::PNG.ggplot(filename, data, plot, width, height, plot_options) 
 

data/share/views/wait.haml

@@ -7,13 +7,17 @@
     overflow: auto
     text-overflow: ellipsis
 
+- title = "#{job.status} #{File.basename(job.name)}"
+:deferjs
+  $('head title').text("#{title}")
+
+
 - progress = false
 .wait.ui.segment.info.message
   %h3.ui.header Waiting on #{format_name File.basename(job.name)}
 
   %span.ui.basic.segment.content.status= job.status
 
-
   - if job.file(:progress).exists?
     .footer.ui.basic.segment
       - progress = job.file(:progress).yaml
@@ -65,22 +69,24 @@
           :deferjs
             $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
 
+
   %hr
-  - if defined? job.info_file and File.exist? job.info_file and @uri.include? job.name
-    - abort_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "abort")
+
+  - if defined?(job.info_file) and File.exist?(job.info_file) and @fullpath.include?(job.name)
+    - abort_url = add_GET_param(remove_GET_param(@fullpath, "_layout"), "_update", "abort")
     %a.ui.button.red.abort(href=abort_url) Abort
     -#- clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "clean")
     -#%a.ui.button.blue.clean(href=clean_url) Clean
   - else
-    - clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "reload")
+    - clean_url = add_GET_param(remove_GET_param(@fullpath, "_layout"), "_update", "reload")
     %a.ui.blue.button.reload(href=clean_url) Reload
 
-  - if @uri.include? job.name
-    - info_url = @uri.sub(/\?.*/,'') + '/info'
-    %a.ui.blue.button.reload(href=info_url) Info
+  - if @fullpath.include?(job.name)
+    - info_url = @fullpath.sub(/\?.*/,'') + '/info'
+    %a.ui.blue.button.reload(href=@fullpath) Info
 
-  - if job.files.any? and @uri.include? job.name
-    - files_url = @uri.sub(/\?.*/,'') + '/files'
+  - if job.files.any? and @fullpath.include? job.name
+    - files_url = @fullpath.sub(/\?.*/,'') + '/files'
     %a.ui.blue.button.reload(href=files_url) Files
 
 - if ! progress
@@ -95,14 +101,15 @@
     }
 
 
-.ui.segment
-  %h3.ui.header Log
-  %ul.step_messages.clean_list
-    - job.messages.reverse.each do |line|
-      - next if line.nil? or line.strip.empty?
-      %li= line
+- if job.messages
+  .ui.segment
+    %h3.ui.header Log
+    %ul.step_messages.clean_list
+      - job.messages.reverse.each do |line|
+        - next if line.nil? or line.strip.empty?
+        %li= line
 
-- if job.dependencies.any?
+- if job.dependencies && job.dependencies.any?
   
   .ui.segment
     %h3.ui.header Dependencies

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.9.1
+  version: 2.0.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-09-14 00:00:00.000000000 Z
+date: 2025-02-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: modular-scale
@@ -1853,7 +1853,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.0.dev
+rubygems_version: 3.5.23
 signing_key: 
 specification_version: 4
 summary: Rbbt Web and REST interfaces