rbbt-rest 1.8.157 → 1.9.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2e4b22bac9c83a30a558edc6a2da6b3472fb4b4fd4e6a656129d80411e2d9e52
-  data.tar.gz: a2a5802a8dab099897fa5cca2f97c208702509bc72200af6a04113f4f49f1e1e
+  metadata.gz: f704f277ce12001953704f8e901241c79f1bc0d6425967ae231455671bfa7879
+  data.tar.gz: 07d4ca572f44e36384bd7595f1c36738b6388c4f3da1fa03827a118b5eed3724
 SHA512:
-  metadata.gz: f389432ce901f5a7b1c7f41a03b84fe89d32c03db44afbfbb8585aa496a96d7651a627e8db90aff39d4411789ed1bcc51ac7ce166d497204b2823e0c00c35eb0
-  data.tar.gz: b7af3754e961b7965fefbcca749dc68f40d02fa2bf498484664591e41f280dc53a9d3ef3e0c95b985e0da844d2d024862e7deb0fbcc4262750b0fec3c525f28b
+  metadata.gz: ca607c13addb28475b071f500a50e9ccac7c13007e765fb044cba6e9f41735a45e0de2ad403984bbaaf36ba662397140f06d542090bb9936981890d4b5b988c5
+  data.tar.gz: d2f72803da7071b5e0d2c743344dc120e7ad56c387ada1d002492ad5b0eeab138b5cd0d630b72af9e5fe8156268d36f65288193c494e2c2ced69c9e6829288b6

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

@@ -20,10 +20,10 @@ module RbbtRESTHelpers
   def old_cache(path, check)
     return false if production?
     return false if check.nil? or check.empty?
-    return false if not File.exists? path
+    return false if not File.exist? path
     check = [check] unless Array === check
     check.each do |file|
-      if not File.exists?(file)
+      if not File.exist?(file)
         return true 
       end
       if File.mtime(file) > File.mtime(path)
@@ -207,7 +207,11 @@ module RbbtRESTHelpers
           data = nil
           excel_file = TmpFile.tmp_file
           tsv.excel(excel_file, :sort_by => @excel_sort_by, :sort_by_cast => @excel_sort_by_cast, :name => true, :remove_links => true)
-          send_file excel_file, :type => 'application/vnd.ms-excel', :filename => 'table.xls'
+          name = tsv_options[:table_id]
+          name ||= "rbbt-table"
+          name = name.sub(/\s/,'_')
+          name = name.sub('.tsv','')
+          send_file excel_file, :type => 'application/vnd.ms-excel', :filename => "#{name}.xls"
         when "heatmap"
           require 'rbbt/util/R'
           tsv, tsv_options = load_tsv(fragment_file)
@@ -270,7 +274,7 @@ data = NULL
           if mime && mime.to_s.include?("text/html")
             halt_html txt || Open.read(fragment_file)
           else
-            if File.exists?(fragment_file)
+            if File.exist?(fragment_file)
               send_file fragment_file
             else
               halt 200, Open.read(fragment_file)
@@ -325,7 +329,7 @@ data = NULL
             raise RbbtRESTHelpers::Retry
           end
 
-          #if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
+          #if File.exist?(step.info_file) and Time.now - File.atime(step.info_file) > 60
           #  Log.debug{ "Checking on #{step.info_file}" }
           #  running = (not step.done?) and step.running?
           #  if FalseClass === running

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

@@ -5,7 +5,7 @@ module RbbtRESTHelpers
   class Retry < Exception; end
 
   def check_step(step)
-    if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
+    if File.exist?(step.info_file) and Time.now - File.atime(step.info_file) > 60
       done = step.done?
       running = done ? false : step.running?
       Log.debug{ "Checking on #{step.info_file} (done: #{done}; running: #{running})" }
@@ -301,7 +301,7 @@ module RbbtRESTHelpers
   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.mkdir_p settings.permalink_dir unless File.exist? settings.permalink_dir
     FileUtils.ln_s(path, dest)
     "/permalink/#{ id }"
   end
@@ -322,36 +322,81 @@ module RbbtRESTHelpers
 
 end
 
-class Haml::Filters::DeferJS < Haml::Filters::Base
+if $haml_6
+  Haml::Template.options[:escape_html] = false
 
-  def render(text)
-    step_path = Thread.current["step_path"]
-    text = "" if text.nil?
-    defer_text =<<-EOF
+  class Haml::Filters::DeferJS < Haml::Filters::TiltBase
+
+    def compile(node)
+      text = node.value[:text]
+      step_path = Thread.current["step_path"]
+      text = "" if text.nil?
+      defer_text =<<-EOF
 %script
   :plain
     defer(function(step_path){
 
 #{text.gsub(/^/,"      ")}
     }, '#{step_path}')
-EOF
-    Haml::Engine.new(defer_text).to_html 
+      EOF
+      node.value[:text] = defer_text
+      compile_with_tilt(node, 'haml')
+    end
   end
-end
 
-class Haml::Filters::Documentation < Haml::Filters::Base
+  class Haml::Filters::Documentation < Haml::Filters::TiltBase
 
-  def render(text)
-    text = "<br/>" if text.strip.empty?
+    def compile(node)
+      text = node.value[:text]
+      text = "<br/>" if text.strip.empty?
 
-    doc_text =<<-EOF
+      doc_text =<<-EOF
 %section.documentation#{ text.gsub(/\s/,'').length < 80 * 10 ? '.short' : ''}
   :markdown
 #{text.gsub(/^/,"    ")}
-    EOF
+      EOF
 
-    Haml::Engine.new(doc_text).to_html  
+      node.value[:text] = doc_text
+      compile_with_tilt(node, 'haml')
+    end
   end
 
-end
+  class Haml::Filters
+    register :deferjs, Haml::Filters::DeferJS
+    register :documentation, Haml::Filters::Documentation
+  end
+else
+	module Haml::Filters::DeferJS
+		include Haml::Filters::Base
+
+		def render(text)
+			step_path = Thread.current["step_path"]
+			text = "" if text.nil?
+			defer_text =<<-EOF
+%script
+  :plain
+    defer(function(step_path){
+#{text.gsub(/^/,"      ")}
+    }, '#{step_path}')
+      EOF
+			Haml::Engine.new(defer_text).to_html 
+		end
+	end
+
+	module Haml::Filters::Documentation
+		include Haml::Filters::Base
+
+		def render(text)
+			text = "<br/>" if text.strip.empty?
 
+			doc_text =<<-EOF
+%section.documentation#{ text.gsub(/\s/,'').length < 80 * 10 ? '.short' : ''}
+  :markdown
+#{text.gsub(/^/,"    ")}
+      EOF
+
+			Haml::Engine.new(doc_text).to_html  
+		end
+
+	end
+end

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

@@ -3,7 +3,6 @@ require 'rbbt/rest/common/cache'
 require 'tilt'
 
 Tilt::SYMBOL_ARRAY_SORTABLE = false
-
 module RbbtRESTHelpers
   def error_for(job, layout = nil)
     if ex = job.info[:exception]
@@ -153,7 +152,8 @@ module RbbtRESTHelpers
               end
             end
             Log.low("Fragment started: #{ fragment_file } - #{Process.pid}")
-            res = capture_haml fragment_code, &block
+            #res = capture_haml fragment_code, &block
+            res = $haml_6 ? capture(&block) : capture_haml(&block)
             Log.low("Fragment writing: #{ fragment_file } - #{Process.pid}")
             Open.write(fragment_file, res)
             Log.low("Fragment done: #{ fragment_file } - #{Process.pid}")
@@ -196,7 +196,7 @@ module RbbtRESTHelpers
           end
         end
       else
-        capture_haml &block
+        $haml_6 ? capture(&block) : capture_haml(&block)
       end
     else
       if link =~ / class=/
@@ -294,7 +294,8 @@ module RbbtRESTHelpers
   def reveal(text, id = nil, options = nil, &block)
     id ||= "rbbt_reveal_" << (rand * 10000).to_i.to_s
 
-    content_html = capture_haml(&block)
+    #content_html = capture_haml(&block)
+    content_html = $haml_6 ? capture(&block) : capture_haml(&block)
 
     options = {} if options.nil?
     options = {:href => "#", "data-reveal-id" => 'modal1', 'attr-reveal_id' => id}.merge(options)

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

@@ -40,7 +40,7 @@ module RbbtRESTHelpers
       md5 = Misc.digest(recorded_js_files * ",")
       filename = settings.file_dir["all_js-#{md5}.js"].find
 
-      if not File.exists?(filename)
+      if not File.exist?(filename)
         Log.debug{ "Regenerating JS Compressed file: #{ filename }" }
 
         text = recorded_js_files.collect{|file| 
@@ -53,7 +53,7 @@ module RbbtRESTHelpers
           "//FILE: #{ File.basename(path) }\n" +  Open.read(path)
         } * "\n"
 
-        FileUtils.mkdir_p File.dirname(filename) unless File.exists? File.dirname(filename)
+        FileUtils.mkdir_p File.dirname(filename) unless File.exist? File.dirname(filename)
         Open.write(filename, Uglifier.compile(text))
       end
 

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

@@ -146,6 +146,32 @@ Quality
 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
@@ -390,7 +416,7 @@ module RbbtRESTHelpers
       tsv = TSV.open(Open.open(file))
     end
 
-    table_options = File.exists?(file + '.table_options') ? YAML.load_file(file + '.table_options') : {}
+    table_options = File.exist?(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, (tsv.entity_options || {}).merge(p.last)) } unless headers.nil?
@@ -402,10 +428,12 @@ module RbbtRESTHelpers
     RbbtRESTHelpers.load_tsv(*args)
   end
 
-  def table(options = {})
+  def table(options = {},&block)
     options = {} if options.nil?
 
-    tsv = yield
+    tsv = $haml_6 ? capture(&block) : block.call
+
+    raise "Use next to return the table" if String === tsv
 
     table_code = options[:table_id] || (rand * 100000).to_i.to_s
     table_code = Entity::REST.clean_element(table_code)

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

@@ -1,6 +1,7 @@
-
 module RbbtRESTHelpers
   class Tabs
+    include RbbtRESTHelpers
+
     attr_accessor :headers, :codes, :content, :classes, :tab_classes
     def initialize(page)
       @page = page
@@ -13,7 +14,7 @@ module RbbtRESTHelpers
       @content ||= {}
 
       if block_given? 
-        html = @page.capture_haml &block
+        html = $haml_6 ? capture(&block) : @page.capture_haml(&block)
       else
         html = nil
       end

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

@@ -57,10 +57,10 @@ module Entity
 
     def self.load_list(entity_type, id, user = nil)
       path = list_file(entity_type, id, user)
-      path = list_file(entity_type, id, :public) unless path != nil and File.exists? path
-      path = list_file(entity_type, id) unless path != nil and File.exists? path
+      path = list_file(entity_type, id, :public) unless path != nil and File.exist? path
+      path = list_file(entity_type, id) unless path != nil and File.exist? path
 
-      raise "List not found: #{ id }" if path.nil? or not File.exists? path
+      raise "List not found: #{ id }" if path.nil? or not File.exist? path
 
       begin
         list = Annotated.load_tsv TSV.open(path)
@@ -79,7 +79,7 @@ module Entity
         begin
           Open.write(path, Annotated.tsv(list, :all).to_s)
         rescue
-          FileUtils.rm path if File.exists? path
+          FileUtils.rm path if File.exist? path
           raise $!
         end
       end
@@ -88,11 +88,11 @@ module Entity
     def self.delete_list(entity_type, id, user)
       path = list_file(entity_type, id, user)
 
-      "This list does not belong to #{ user }: #{[entity_type, id] * ": "}" unless File.exists? path
+      "This list does not belong to #{ user }: #{[entity_type, id] * ": "}" unless File.exist? path
 
       Misc.lock path do
         begin
-          FileUtils.rm path if File.exists? path
+          FileUtils.rm path if File.exist? path
         rescue
           raise $!
         end

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

@@ -39,7 +39,7 @@ module EntityRESTHelpers
       path.annotate check_file 
       return false unless check_file.exists?
     else
-      return false unless File.exists?(check_file)
+      return false unless File.exist?(check_file)
     end
 
     reject?(check_file, binding)

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

@@ -57,8 +57,8 @@ module Entity
 
     def self.load_map(entity_type, column, id, user = nil)
       path = map_file(entity_type, column, id, user)
-      path = map_file(entity_type, column, id, :public) unless path != nil and File.exists? path
-      path = map_file(entity_type, column, id) unless path != nil and File.exists? path
+      path = map_file(entity_type, column, id, :public) unless path != nil and File.exist? path
+      path = map_file(entity_type, column, id) unless path != nil and File.exist? path
 
       begin
         RbbtRESTHelpers.load_tsv(path).first
@@ -75,7 +75,7 @@ module Entity
         begin
           RbbtRESTHelpers.save_tsv(map, path)
         rescue
-          FileUtils.rm path if path and File.exists? path
+          FileUtils.rm path if path and File.exist? path
           raise $!
         end
       end
@@ -84,11 +84,11 @@ module Entity
     def self.delete_map(entity_type, column, id, user)
       path = map_file(entity_type, column, id, user)
 
-      "This map does not belong to #{ user }: #{[entity_type, column, id] * ": "}" unless File.exists? path
+      "This map does not belong to #{ user }: #{[entity_type, column, id] * ": "}" unless File.exist? path
 
       Misc.lock path do
         begin
-          FileUtils.rm path if File.exists? path
+          FileUtils.rm path if File.exist? path
         rescue
           raise $!
         end

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

@@ -189,7 +189,7 @@ module Entity
       reuse = options.delete("reuse") if reuse.nil?
       reuse = true if reuse.nil?
 
-      Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exists?(Entity::List.list_file(entity_type.to_s, id))
+      Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exist?(Entity::List.list_file(entity_type.to_s, id))
 
       klasses = self.klasses
       klasses << 'entity_list'
@@ -212,7 +212,7 @@ module Entity
       reuse = options.delete("reuse") if reuse.nil?
       reuse = true if reuse.nil?
 
-      Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exists? Entity::List.list_file(entity_type.to_s, id, self)
+      Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exist? Entity::List.list_file(entity_type.to_s, id, self)
 
       klasses = self.klasses
       klasses << 'entity_list_action'

data/lib/rbbt/rest/entity.rb

@@ -134,10 +134,10 @@ module Sinatra
           when :raw, :literal
             content_type "text/tab-separated-values"
             user_file = Entity::List.list_file(entity_type.split(":").first, list_id, user)
-            send_file user_file if File.exists? user_file
+            send_file user_file if File.exist? user_file
 
             global_file = Entity::List.list_file(entity_type.split(":").first, list_id, nil)
-            send_file global_file if File.exists? global_file
+            send_file global_file if File.exist? global_file
 
             raise "List file not found: #{ list_id }"
           when :json
@@ -296,21 +296,21 @@ module Sinatra
           case @format
           when :name
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
+            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
             new = TSV.open(file).change_key "Associated Gene Name"
             new_id = map_id << " [Names]"
             Entity::Map.save_map(entity_type, column, new_id, new, user)
             redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
           when :ensembl
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
+            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
             new = TSV.open(file).change_key "Ensembl Gene ID"
             new_id = map_id << " [Ensembl]"
             Entity::Map.save_map(entity_type, column, new_id, new, user)
             redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
           when :pvalue_score
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
+            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
             tsv =  TSV.open(file)
             tsv.process tsv.fields.first do |value|
               value = value.flatten.first if Array === value
@@ -325,7 +325,7 @@ module Sinatra
             redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
           when :ranks
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
+            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
             tsv =  TSV.open(file, :cast => :to_f)
             new = tsv.ranks_for(tsv.fields.first)
             new_id = map_id << " [Ranks]"
@@ -334,7 +334,7 @@ module Sinatra
             redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
           when :invert_ranks
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
+            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
             tsv =  TSV.open(file)
             size = tsv.size
             tsv.process "Rank" do |v|
@@ -351,15 +351,15 @@ module Sinatra
           when :raw, :literal
             content_type "text/tab-separated-values"
             user_file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            send_file user_file if File.exists? user_file
+            send_file user_file if File.exist? user_file
 
             global_file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil)
-            send_file global_file if File.exists? global_file
+            send_file global_file if File.exist? global_file
 
             raise "Map file not found: #{ map_id }"
           when :json
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
-            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
+            file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
 
             content_type "application/json"
             tsv = TSV.open(file)
@@ -413,13 +413,13 @@ module Sinatra
           column = Entity::REST.restore_element(column)
 
           file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, user)
-          file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, nil) unless File.exists? file1
-          raise "Map not found: #{ map1 }" unless File.exists? file1
+          file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, nil) unless File.exist? file1
+          raise "Map not found: #{ map1 }" unless File.exist? file1
           tsv1 =  TSV.open(file1, :cast => :to_f) 
 
           file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, user)
-          file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, nil) unless File.exists? file2
-          raise "Map not found: #{ map2 } - #{ file2 }" unless File.exists? file2
+          file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, nil) unless File.exist? file2
+          raise "Map not found: #{ map2 } - #{ file2 }" unless File.exist? file2
           tsv2 =  TSV.open(file2, :cast => :to_f)
 
           tsv1 = tsv1.select :key => tsv2.keys

data/lib/rbbt/rest/main.rb

@@ -1,3 +1,6 @@
+require 'haml'
+$haml_6 = Gem::Version.new(Haml::VERSION) >= Gem::Version.new("6.0.0")
+
 require 'rbbt/rest/common/locate'
 require 'rbbt/rest/common/resources'
 require 'rbbt/rest/common/users'
@@ -14,6 +17,7 @@ require 'json'
 require 'nakayoshi_fork'
 
 Rbbt.add_version(__FILE__)
+
 module Sinatra
   module RbbtRESTMain
 
@@ -55,7 +59,10 @@ module Sinatra
 
         set :environment, ENV["RACK_ENV"].to_sym if ENV["RACK_ENV"]
 
-        attr_accessor :ajax, :layout, :format, :size, :update, :cache_type, :_, :profile
+        attr_accessor :ajax, :layout, :size, :update, :cache_type, :_, :profile
+
+        # This collides with a function in sinatra
+        #attr_accessor :format
 
 
         enable :cross_origin
@@ -121,7 +128,7 @@ module Sinatra
             printer = RubyProf::MultiPrinter.new(result)
             dir = TmpFile.tmp_file
             dir = settings.file_dir
-            FileUtils.mkdir_p dir unless File.exists? dir
+            FileUtils.mkdir_p dir unless File.exist? dir
             printer.print(:path => dir, :profile => 'profile')
             Log.info{ "Profile saved at #{ dir }: #{@uri}" }
           end

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

@@ -52,8 +52,9 @@ module WorkflowRESTHelpers
 
   def execution_type(workflow, task)
     export = type_of_export(workflow, task)
+    return :slurm if ENV["RBBT_REST_USE_SLURM"] == 'true'
     return cache_type if cache_type
-    return :sync if export == :exec and format == :html
+    return :sync if export == :exec and @format == :html
     return export if export == :exec 
     return :asynchronous
   end
@@ -82,7 +83,7 @@ module WorkflowRESTHelpers
   end
 
   def show_exec_result(result, workflow, task)
-    case format.to_sym
+    case @format.to_sym
     when :html
       show_result_html result, workflow, task, nil
     when :json
@@ -108,14 +109,14 @@ module WorkflowRESTHelpers
     when :jobname
       halt 200, nil
     else
-      raise "Unsupported format: #{ format }"
+      raise "Unsupported format: #{ @format }"
     end
   end
 
   def show_result(job, workflow, task, params = nil)
     return show_result_html nil, workflow, task, job.name, job, params if @fragment
 
-    case format.to_sym
+    case @format.to_sym
     when :html
       show_result_html :load, workflow, task, job.name, job, params
     when :table
@@ -151,7 +152,7 @@ module WorkflowRESTHelpers
       if job.path
         if Open.remote? job.path
           Open.open(job.path, :nocache => true)
-        elsif File.exists? job.path
+        elsif File.exist? job.path
           send_file(job.path, :filename => (params[:filename] || File.basename(job.path)))
         else
           halt 200, job.load
@@ -183,7 +184,7 @@ module WorkflowRESTHelpers
       EOF
       send_file png_file, :type => 'image/png', :filename => job.name + ".heatmap.png"
     else
-      raise "Unsupported format: #{ format }"
+      raise "Unsupported format: #{ @format }"
     end
   end
 
@@ -249,7 +250,7 @@ module WorkflowRESTHelpers
           job.join
         end
 
-        if format == :jobname
+        if @format == :jobname
           job.name
         else
           job_url = job.respond_to?(:url)? job.url : File.join("/", workflow.to_s, task, job.name)
@@ -270,7 +271,7 @@ module WorkflowRESTHelpers
         # $rest_cache_semaphore is defined in rbbt-util etc/app.d/semaphores.rb
         job.fork($rest_cache_semaphore) unless job.started?
 
-        if format == :jobname
+        if @format == :jobname
           job.soft_grace
           content_type :text
           job.name
@@ -283,6 +284,15 @@ module WorkflowRESTHelpers
       rescue Exception
         Log.exception $!
       end
+    when :slurm
+      require 'rbbt/hpc'
+      batch_system = ENV["BATCH_SYSTEM"] || "SLURM"
+      system = HPC.batch_system batch_system
+      system.orchestrate_job(job, {}) 
+      job_url = job.respond_to?(:url)? job.url : File.join("/", workflow.to_s, task, job.name)
+      job_url += "?_format=#{@format}" if @format
+      iii job_url
+      redirect to(job_url)
     else
       raise "Unsupported execution_type: #{ execution_type }"
     end
@@ -291,7 +301,7 @@ module WorkflowRESTHelpers
   def recursive_clean_job(workflow, job)
     job.recursive_clean
 
-    if format == :jobname
+    if @format == :jobname
       halt 200, job.name
     elsif ajax
       halt 200
@@ -309,9 +319,9 @@ module WorkflowRESTHelpers
   def clean_job(workflow, job)
     job.clean
 
-    if format == :jobname
+    if @format == :jobname
       halt 200, job.name
-    elsif ajax or format == :json
+    elsif @ajax or @format == :json
       halt 200
     else
       redirect to(File.join("/", workflow.to_s, job.task_name.to_s))

data/lib/rbbt/rest/workflow.rb

@@ -41,10 +41,10 @@ module Sinatra
         workflow.export *workflow.tasks.keys
       end
 
-      self.instance_eval workflow.libdir.lib['sinatra.rb'].read, workflow.libdir.lib['sinatra.rb'].find if workflow.respond_to?(:libdir) and  File.exists? workflow.libdir.lib['sinatra.rb']
+      self.instance_eval workflow.libdir.lib['sinatra.rb'].read, workflow.libdir.lib['sinatra.rb'].find if workflow.respond_to?(:libdir) and  File.exist? workflow.libdir.lib['sinatra.rb']
 
       get "/#{workflow.to_s}" do
-        case format
+        case @format
         when :json
           content_type "application/json"
 
@@ -56,14 +56,14 @@ module Sinatra
       end
 
       get "/#{workflow.to_s}/documentation" do
-        case format
+        case @format
         when :html
           workflow_render('tasks', workflow)
         when :json
           content_type "application/json"
           workflow.documentation.to_json
         else
-          raise "Unsupported format specified: #{ format }"
+          raise "Unsupported format specified: #{ @format }"
         end
       end
 
@@ -72,14 +72,14 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
-        case format
+        case @format
         when :html
           workflow_render('task_info', workflow, nil, :cache => false )
         when :json
           content_type "application/json"
           workflow.task_info(task.to_sym).to_json
         else
-          raise "Unsupported format specified: #{ format }"
+          raise "Unsupported format specified: #{ @format }"
         end
       end
 
@@ -88,14 +88,14 @@ module Sinatra
 
         raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
 
-        case format
+        case @format
         when :html
           workflow_render('task_dependencies', workflow)
         when :json
           content_type "application/json"
           workflow.task_dependencies[task.to_sym].to_json
         else
-          raise "Unsupported format specified: #{ format }"
+          raise "Unsupported format specified: #{ @format }"
         end
       end
 
@@ -116,7 +116,7 @@ module Sinatra
         
         task_parameters[:jobname] = jobname
 
-        if complete_input_set(workflow, task, task_parameters) || format != :html || jobname
+        if complete_input_set(workflow, task, task_parameters) || @format != :html || jobname
           issue_job(workflow, task, jobname, task_parameters)
         else
           workflow_render('form', workflow, task, task_parameters)
@@ -185,7 +185,7 @@ module Sinatra
                 error_for job
               when error
                 error_for job
-              when (exec_type == :asynchronous or exec_type == :async)
+              when (exec_type == :asynchronous or exec_type == :async or exec_type == :slurm)
                 case @format.to_s
                 when 'json', 'raw', 'binary'
                   halt 202
@@ -226,7 +226,7 @@ module Sinatra
 
         halt 404, "Job not found: #{job.path} (#{job.status})" if job.status == :noinfo and not job.done?
 
-        case format
+        case @format
         when :html
           workflow_render('job_info', workflow, task, :job => job, :info => job.info)
         when :input_bundle
@@ -262,7 +262,7 @@ module Sinatra
           end
           halt 200, info_json.to_json
         else
-          raise "Unsupported format specified: #{ format }"
+          raise "Unsupported format specified: #{ @format }"
         end
       end
 
@@ -276,14 +276,14 @@ module Sinatra
 
         job = workflow.fast_load_id(File.join(task, job))
 
-        case format
+        case @format
         when :html
           workflow_render('job_files', workflow, task, :info => job.info, :job => job)
         when :json
           content_type "application/json"
           job.files.to_json
         else
-          raise "Unsupported format specified: #{ format }"
+          raise "Unsupported format specified: #{ @format }"
         end
       end
 

data/share/views/compass/app.sass

@@ -141,7 +141,7 @@ $cyan: rgba(50, 211, 255, 1)
 .dependencies, .job_info
   .status
     color: $cyan
-  .status.waiting, .status.noinfo
+  .status.waiting, .status.noinfo, .status.cleaned
     color: $yellow
   .status.started
     color: $cyan

data/share/views/entity_partials/action_card.haml

@@ -22,7 +22,7 @@
       - when String
         %p= card.description
       - when Proc
-        = capture_haml &card.description
+        = capture &card.description
       - else
         - raise "Unknown description: #{fff card.description}"
 
@@ -36,7 +36,7 @@
         - inputs, input_block = input
         - if inputs.select{|input| @params[input.to_s].nil? }.any?
           - require_parameters = true
-          - exception_html = capture_haml  &input_block
+          - exception_html = capture  &input_block
           - break
 
       - else
@@ -51,5 +51,5 @@
       - if require_parameters
         .ui.message.warning Please configure the parameters to execute the action
       - else
-        = capture_haml &block
+        = capture &block
 

data/share/views/entity_partials/entity_card.haml

@@ -96,7 +96,7 @@
       - if defined? block and block
         /-- description block --
         .description.ui.basic.segment<
-          = capture_haml &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_list_card.haml

@@ -98,7 +98,7 @@
       - if defined? block and block
         /-- description block --
         .description.ui.basic.segment<
-          = capture_haml &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

@@ -30,7 +30,7 @@
               - pvalue = pvalue.collect{|p| p == 0 ? 0.000000000000000000001 : p }
               = resource map_id + '.qqplot.png', nil, :image do |file|
                 = fragment do
-                  - FileUtils.mkdir_p File.dirname(file) unless File.exists? File.dirname(file)
+                  - FileUtils.mkdir_p File.dirname(file) unless File.exist? File.dirname(file)
                   :ruby
                     script =<<-EOF
                       library(ggplot2)

data/share/views/form.haml

@@ -31,7 +31,7 @@
           - name = File.basename(example_dir)
           - task_info = workflow.task_info task
           - inputs = Workflow.load_inputs(example_dir, task_info[:inputs], task_info[:input_types])
-          - inputs.each{|k,v| v.replace Open.read(v) if String === v and File.exists? v }
+          - inputs.each{|k,v| v.replace Open.read(v) if String === v and File.exist? v }
           - new = {}
           - inputs.each{|k,v| v.filename = nil if TSV === v ; v = v * "\n" if Array === v; new[k] = v.to_s }
           - inputs = new

data/share/views/job_result/tsv.haml

@@ -4,7 +4,7 @@
   - page = result.size > 50 ? "1" : nil
 
   = table :table_id => table_id, :page => page, :table_class => table_class, :row_ids => :use, :table_url => jobname ? to(File.join('/', workflow.to_s, task, jobname)) : nil do
-    - result
+    - next result
 
   -#
     - begin

data/share/views/partials/dependencies.haml

@@ -4,8 +4,11 @@
 %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)
 

data/share/views/wait.haml

@@ -66,7 +66,7 @@
             $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
 
   %hr
-  - if defined? job.info_file and File.exists? job.info_file and @uri.include? job.name
+  - 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")
     %a.ui.button.red.abort(href=abort_url) Abort
     -#- clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "clean")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.157
+  version: 1.9.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-03-07 00:00:00.000000000 Z
+date: 2023-09-14 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: 3.1.4
+rubygems_version: 3.5.0.dev
 signing_key: 
 specification_version: 4
 summary: Rbbt Web and REST interfaces