rbbt-rest 1.9.0 → 1.9.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: ff6ec603aa45072af8aa5cf99203bac5c63590f657b6f96d38cb172beee4ee09
+  metadata.gz: f704f277ce12001953704f8e901241c79f1bc0d6425967ae231455671bfa7879
+  data.tar.gz: 07d4ca572f44e36384bd7595f1c36738b6388c4f3da1fa03827a118b5eed3724
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+  data.tar.gz: d2f72803da7071b5e0d2c743344dc120e7ad56c387ada1d002492ad5b0eeab138b5cd0d630b72af9e5fe8156268d36f65288193c494e2c2ced69c9e6829288b6

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

@@ -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)

data/lib/rbbt/rest/main.rb

@@ -59,7 +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

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
@@ -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

@@ -44,7 +44,7 @@ module Sinatra
       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/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)
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.9.0
+  version: 1.9.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-03-17 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: 3.4.8
+rubygems_version: 3.5.0.dev
 signing_key: 
 specification_version: 4
 summary: Rbbt Web and REST interfaces