rbbt-rest 1.8.103 → 1.8.104

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 72db9cac8d95433bd7eaa8ceaa4751642898af76
-  data.tar.gz: 5749497c739b60c8f07517009b46a45824736e05
+  metadata.gz: 48bc5fff36fc2884fac2ce8c93cc7c1986194bd5
+  data.tar.gz: 296b0484af0c3a2cc80360eea0210e77f16f46e9
 SHA512:
-  metadata.gz: 6c7de30acecf251bb220d557f67f5b81cdc91db7c11a74e17518823918b3788a96d17c8d46ea7b6b560a9a49dc126089f97f038515ab9fb903dbd658763f1a94
-  data.tar.gz: 0f6da7889bcd4095811b4a66b478b5cd5f8fd8c44099ab52f4b3322ff3a7ba482b3a16a275fe62b933277ffcb83bcb7479b6a6856578a943ee74967bf491bf57
+  metadata.gz: c9f2242fc4c7cac714684a0007d0fce4391a111a6dde2c2b9ac0cc7293b92d7d55f42d584cf9f3df86b4a5de388bbcc67bb5589d402b6bbd3d9b52ff2553f202
+  data.tar.gz: 23b19c9ce56abb4c0109ebe34fa539372f2135dfc0a78accb8a97bb8cccd392d821ba938412fa69569a3e2d900f38b1dd07b45235a143821111fe082af38051b

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

@@ -86,6 +86,7 @@ module RbbtRESTHelpers
 
     step.instance_variable_set(:@url, clean_url)
     step.instance_variable_set(:@url_path, URI(clean_url).path)
+    step.clean if step.error? or step.aborted?
 
     Thread.current["step_path"] = step.path
     # Issue
@@ -103,7 +104,7 @@ module RbbtRESTHelpers
 
     if @fragment
       fragment_file = step.file(@fragment)
-      if File.exists?(fragment_file)
+      if Open.exists?(fragment_file)
         case @format.to_s
         when "query-entity"
           tsv, table_options = load_tsv(fragment_file, true)
@@ -206,13 +207,13 @@ module RbbtRESTHelpers
           mime = nil
           Open.open(fragment_file) do |io|
             begin
-              mime = MimeMagic.by_path(io) 
+              mime = MimeMagic.by_path(fragment_file) 
               if mime.nil?
                 io.rewind
                 mime = MimeMagic.by_magic(io) 
               end
               if mime.nil?
-                io.rewind
+                io.rewind if IO === io
                 mime = "text/tab-separated-values" if io.gets =~ /^#/ and io.gets.include? "\t"
               end
             rescue Exception
@@ -239,7 +240,11 @@ module RbbtRESTHelpers
             content_type "text/plain"
           end
 
-          send_file fragment_file
+          if File.exists? fragment_file
+            send_file fragment_file
+          else
+            halt 200, Open.read(fragment_file)
+          end
         end
       elsif Open.exists?(fragment_file + '.error') 
         klass, _sep, message = Open.read(fragment_file + '.error').partition(": ")

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

@@ -149,6 +149,7 @@ module RbbtRESTHelpers
           begin
             Log.low("Fragment started: #{ fragment_file } - #{Process.pid}")
             res = capture_haml fragment_code, &block
+            Log.low("Fragment writing: #{ fragment_file } - #{Process.pid}")
             Open.write(fragment_file, res)
             Log.low("Fragment done: #{ fragment_file } - #{Process.pid}")
           rescue Exception
@@ -156,10 +157,10 @@ module RbbtRESTHelpers
             Open.write(fragment_file + '.backtrace', $!.backtrace * "\n") if $!.backtrace
             Log.error("Error in fragment: #{ fragment_file }")
             Log.exception $!
-            FileUtils.rm pid_file if File.exists? pid_file
+            Open.rm pid_file if Open.exists? pid_file
             Kernel.exit! -1
           ensure
-            FileUtils.rm pid_file if File.exists? pid_file
+            Open.rm pid_file if Open.exists? pid_file
           end
           Kernel.exit! 0
         }
@@ -232,7 +233,7 @@ module RbbtRESTHelpers
       f = settings.file_dir[filename].find
     end
 
-    FileUtils.mkdir_p(File.dirname(f))
+    Open.mkdir(File.dirname(f))
 
     yield(f)
 
@@ -270,8 +271,6 @@ module RbbtRESTHelpers
       f = settings.file_dir[filename].find
     end
 
-    FileUtils.mkdir_p(File.dirname(f))
-
     Open.write(f, object.to_json)
 
     if promise

data/lib/rbbt/rest/monitor.rb

@@ -25,6 +25,18 @@ module Sinatra
             template_render('monitor/jobs', {:workflow => workflow, :job_info => job_info}, nil, :cache_type => :none)
           end
         end
+
+        get '/jobs/:workflow/:task' do
+          workflow = params[:workflow]
+          task = params[:task]
+          job_info = Rbbt.job_info(workflow, task)
+          case @format
+          when :json
+            halt 200, job_info.to_json
+          else
+            template_render('monitor/jobs', {:workflow => workflow, :job_info => job_info}, nil, :cache_type => :none)
+          end
+        end
       end
     end
   end

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

@@ -28,7 +28,6 @@ module WorkflowRESTHelpers
       cache_type = execution_type(workflow, task)
       server_key = $app_name
       html_dir = job.file('.html')
-      FileUtils.mkdir_p html_dir.find unless File.exists? html_dir.find
       other_params = params.dup
       other_params.delete_if{|k,v| k[0] == "_"}
       other_params.delete :result

data/share/views/form.haml

@@ -14,6 +14,7 @@
         :markdown
           #{task_info[:description]}
 
+  %a.ui.button(href="/jobs/#{workflow}/#{task}") View jobs
   .form.action_parameters.ui.segment
     = partial_render('partials/form', :id => id, :action => action, :method => 'post', :bundle => true,
       :enctype => "multipart/form-data", :info => task_info, :klass => 'workflow_task', :locals => locals)

data/share/views/job_info.haml

@@ -37,7 +37,8 @@
             var info = {};
             info[key] = inputs;
             rbbt.LS.store('autofill', info);
-            var url = '/' + workflow + '/' + task_name;
+            var url = '../../../' + workflow + '/' + task_name;
+            console.log(url)
             window.location = rbbt.url_add_script_name(url);
           })
         %dl

data/share/views/monitor/jobs.haml

@@ -1,8 +1,21 @@
 %h2 #{ workflow.to_s } jobs
 
-- tsv = TSV.setup({}, :key_field => "Name", :fields => ["Task", "Status", "Pid", "Start"], :type => :list, :unnamed => true)
+- all = params.include?(:all) && params[:all].to_s == 'true'
+- inputs = params.include?(:inputs) ?  params[:inputs].split(/[,\|\s]/) : []
+
+- if not all
+  %a.ui.blue.button(href='?all=true') Include done
+
+= action_parameters :all => all do |all|
+  - input :inputs, :text, "Inputs or info fields to show"
+  - input :all, :hidden, "Show all", all
+  
+- fields = ["Info", "Task", "Status"]
+- tsv = TSV.setup({}, :key_field => "Name", :fields => fields + inputs, :type => :list, :unnamed => true)
 - job_info.each do |file, info|
-  - next if info[:done]
+  - next if info[:done] unless all
+  - rec_inputs = nil
+  - job_inputs = nil
   - status, pid, name, start = Step.step_info(file).values_at :status, :pid, :name, :start_time
   - status = html_tag("span", status, :class => status.to_s.split(">").last)
   - task = info[:task]
@@ -11,7 +24,27 @@
     - pid = html_tag("span", pid, :class => 'alive')
   - else
     - pid = html_tag("span", pid, :class => 'dead') 
-  - tsv[link] = [task, status, pid, start]
+  - info_link = html_tag("a", "info", :href => "/" << [workflow, task, name, "info"] * "/")
+  - values = [info_link, task, status]
+  - if inputs.any?
+    - wf = Kernel.const_get(workflow)
+    - step = Workflow.fast_load_step(file)
+    - info = step.info
+    - info = IndiferentHash.setup(info)
+    - inputs.each do |i|
+      - value = nil
+      - if info.include? i
+        - value = info[i]
+      - else
+        - job_inputs ||= IndiferentHash.setup((step.inputs || {}).to_hash)
+        - if job_inputs.include?(i)
+          - value = inputs[i]
+        - else
+          - rec_inputs ||= IndiferentHash.setup(step.recursive_inputs.to_hash)
+          - value = rec_inputs[i] if rec_inputs.include? i
+      - values << value
+  - tsv[link] = values
 
-= tsv2html tsv
+= table do
+  - tsv
 

data/share/views/wait.haml

@@ -67,14 +67,16 @@
 
   %hr
   - if defined? job.info_file and File.exists? job.info_file and request.env["REQUEST_URI"].include? job.name
-    - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "clean")
-    %a.ui.button.blue.clean(href=clean_url) Clean
+    - abort_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "abort")
+    %a.ui.button.red.abort(href=abort_url) Abort
+    -#- clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "clean")
+    -#%a.ui.button.blue.clean(href=clean_url) Clean
   - else
     - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "reload")
     %a.ui.blue.button.reload(href=clean_url) Reload
 
-  - info_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/info'
   - if request.env["REQUEST_URI"].include? job.name
+    - info_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/info'
     %a.ui.blue.button.reload(href=info_url) Info
 
   - if job.files.any? and request.env["REQUEST_URI"].include? job.name

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.103
+  version: 1.8.104
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-26 00:00:00.000000000 Z
+date: 2018-12-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake