rbbt-rest 1.8.76 → 1.8.77

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e6876aeaa338af02a3200b7aa840fcb088f39a2e
-  data.tar.gz: daf4ef23af0f3062a811930e889e12598b4c215d
+  metadata.gz: f1de6fcf8b994e77b6a88ce299f4e017e04df807
+  data.tar.gz: ed627370f0aa5a4470b241537e6a484e068787cd
 SHA512:
-  metadata.gz: 2d67fb7ebae9300c5ee035fe03e2b493d3351228027077e9d06ed83804756a3bf78b781a3840642d3a83e50293bcfe2b271947e92c5b2f7fcbaf184bd18ef7ac
-  data.tar.gz: 3a4d6c113b12952e6c9b5afa86e5dd62f6572c52f78efbdfc7d4e43365fc8f470281accc9a36afb485b767bf13953ec42219e314704b2a51d259ef497924fca3
+  metadata.gz: 19d7a35ede5f54282b6032c882c52ee082118d918b7ef5b9413a5695056a7925aedc46e8be285b76690c75cd9e58012d5541d6f9dfa3c34e65671720c95b4718
+  data.tar.gz: ec57136fc071436a09ee66becf750eafbc2768d2782b3cf76cdefb88aaed32079801528055686d4260b06ed1a881c5310df8568b4ddc02cdda3797adc81e93ec

data/lib/rbbt/rest/workflow.rb

@@ -237,7 +237,7 @@ module Sinatra
 
         case format
         when :html
-          workflow_render('job_files', workflow, task, :info => job.info)
+          workflow_render('job_files', workflow, task, :info => job.info, :job => job)
         when :json
           content_type "application/json"
           job.files.to_json

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

@@ -31,6 +31,7 @@ module WorkflowRESTHelpers
       other_params = params.dup
       other_params.delete_if{|k,v| k[0] == "_"}
       other_params.delete :result
+      other_params[:template_file] = template_file
       cache_file = html_dir[server_key + "_" << Misc.obj2digest(other_params)]
       cache_type = false if params[:cache] == FalseClass
       render(template_file, locals, layout_file, [task,workflow,job.name] * "-", :cache_type => cache_type, :cache_file => cache_file)

data/share/views/compass/app.sass

@@ -129,6 +129,9 @@ dl > dd
   margin-left: 1em
 
 
+ul.dependencies
+  padding-left: 1em
+
 .dependencies, .job_info
   .status
     color: gold
@@ -153,3 +156,5 @@ dl > dd
   max-height: 800px
   overflow: auto
 
+.job_control
+  margin-bottom: 2em

data/share/views/error.haml

@@ -14,6 +14,9 @@
 
   - info_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/info'
   %a.ui.blue.button.reload(href=info_url) Info
+  - if job.files.any?
+    - files_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/files'
+    %a.ui.blue.button.reload(href=files_url) Info
 
 - backtrace = job.info[:backtrace]
 - if backtrace and backtrace.any?

data/share/views/job_files.haml

@@ -0,0 +1,24 @@
+
+- files = job.files 
+- task = job.task_name
+- workflow = job.workflow
+- jobname = job.name
+- files.reject!{|f| File.basename(File.dirname(f)) == ".html"}
+
+- if files.any?
+  - files_by_dir = {}
+  - files.each do |file|
+    - dir = File.dirname(file)
+    - files_by_dir[dir] ||= []
+    - files_by_dir[dir]  << file
+
+  - (files_by_dir["."] || []).sort.each do |file|
+    %a.small.ui.button(href="/#{[workflow.to_s, task, jobname, "file", file] * "/"}")= file
+  - (files_by_dir.keys - ["."]).each do |dir|
+    %dl
+      %dt.ui.header #{dir}/
+      %dd
+        .ui.buttons
+          - files_by_dir[dir].each do |file|
+            %a.small.ui.button(href="/#{[workflow.to_s, task, jobname, "file", file] * "/"}")= File.basename(file)
+          

data/share/views/job_result/job_control.haml

@@ -1,11 +1,11 @@
-%dl
-  %dt.ui.header Job control
-  %dd.job_control
-    .ui.buttons
-      %a.ui.small.button(href="/#{[workflow.to_s, task, jobname] * "/"}?_update=clean") clean job
-      %a.ui.small.button(href="/#{[workflow.to_s, task, jobname, "info"] * "/"}") job info
-      %a.ui.small.button(href="/#{[workflow.to_s, task, jobname] * "/"}?_format=raw") get raw result file
+.ui.buttons.job_control
+  %a.ui.small.basic.red.button(href="/#{[workflow.to_s, task, jobname] * "/"}?_update=clean") clean job
+  %a.ui.small.basic.blue.button(href="/#{[workflow.to_s, task, jobname, "info"] * "/"}") job info
+  - if job.files.any?
+    %a.ui.small.basic.blue.button(href="/#{[workflow.to_s, task, jobname, "files"] * "/"}") job files
+  %a.ui.small.basic.blue.button(href="/#{[workflow.to_s, task, jobname] * "/"}?_format=raw") get raw result file
 
+-#
   - files = job.files 
   - files.reject!{|f| File.basename(File.dirname(f)) == ".html"}
 

data/share/views/partials/dependencies.haml

@@ -12,7 +12,19 @@
     - if dep.file(:progress).exists?
       - pgr = dep.file(:progress).yaml
       - if pgr[:last_percent]
-        - pgr_str = " - " + pgr[:last_percent].to_s + "%"
+        - 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
       - else
         - pgr_str = " - " + pgr[:ticks].to_s 
       - status = dep_status.to_s + pgr_str

data/share/views/public/js/rbbt.plots/rbbt.plots.aes.js

@@ -16,7 +16,7 @@ rbbt.plots.aes.map_aesthetic = function(aes, mapper, map_obj){
         }
       }
       aes.push(0)
-      return get_gradient(aes, '#EABD5D', '#40324F')
+      return get_gradient(aes, '#40324F', '#EABD5D')
     case 'sign-gradient':
       if (map_obj){
         if (typeof aes == 'object')
@@ -24,7 +24,7 @@ rbbt.plots.aes.map_aesthetic = function(aes, mapper, map_obj){
         else
           aes = map_obj[aes]
       }
-      return get_sign_gradient(aes, '#EABD5D', '#DDD', '#40324F')
+      return get_sign_gradient(aes, '#40324F', '#DDD', '#EABD5D')
     case 'map':
       if (typeof aes == 'object')
         return aes.map(function(value){ if (value !== undefined && value != null ) value = value.toString(); return map_obj[value] })

data/share/views/public/js/rbbt.plots/rbbt.plots.graph.adapters.js

@@ -105,6 +105,14 @@ rbbt.plots.graph.view_cytoscapejs = function(graph_model, elem, style, layout, e
     style: { 'line-color': 'data(color)',
              'target-arrow-color': 'data(color)'}
   },
+  {
+    selector: 'edge[opacity]',
+    style: { 'opacity': 'data(opacity)'}
+  },
+  {
+    selector: 'edge[width]',
+    style: { 'width': 'data(width)'}
+  },
   {
     selector: 'edge[target-arrow-shape]',
     style: { 'target-arrow-shape': 'data(target-arrow-shape)'}

data/share/views/wait.haml

@@ -52,6 +52,22 @@
           :deferjs
             $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
 
+  %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
+  - 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'
+  %a.ui.blue.button.reload(href=info_url) Info
+
+  - if job.files.any?
+    - files_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/files'
+    %a.ui.blue.button.reload(href=files_url) Files
+
+
 .ui.segment
   %h3.ui.header Log
   %ul.step_messages.clean_list

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.76
+  version: 1.8.77
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-11-09 00:00:00.000000000 Z
+date: 2017-11-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -226,6 +226,7 @@ files:
 - share/views/help/UI.haml
 - share/views/help/entity.haml
 - share/views/help/workflow.haml
+- share/views/job_files.haml
 - share/views/job_info.haml
 - share/views/job_result.haml
 - share/views/job_result/annotations.haml
@@ -1865,7 +1866,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: Rbbt Web and REST interfaces