rbbt-rest 1.8.99 → 1.8.100

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ad6482309191ee32ab32aceb94037c51ccf8b952
-  data.tar.gz: c24b8bce4a0f1ce91e9fa5e63ed9eca65d380e42
+  metadata.gz: 6e300de985d4e401a9ade4802219274d354e318b
+  data.tar.gz: 698553ac0867819d9ac1b63eebfa92111125adc0
 SHA512:
-  metadata.gz: 51f84013c9d5d897e0bc174d3a1e1ac2f7a86d2c70b5bb6b9b4e772c097b92e508858dd40168eced7cc30999cbdc735ca368c797f595afcb9b1bea4b16c0fb81
-  data.tar.gz: e61fbef82b893c88f2b0413cf610b896e837e43222e358be3e6074e3cb69344210b685ddaf2cd2d97acc68f1dd3ae05c93e1a6aa21bff171dbe1ffaf96c9086b
+  metadata.gz: bb8f336021a91d2fd6ca900416a147d272a054efeabdde75744e57f95609f305bd80ab08746b24b1a57e85b50fb316bfce1779216dc4ab0e2bbb28712059d06b
+  data.tar.gz: 897331ed434c75939f6fa368b61b66705f10566d28dafdf90fc9bae35ac6be2c3924300a8677653a9e76d8df39205bcf9cb08773e804d3d4084125962a6c2def

data/Rakefile

@@ -17,6 +17,7 @@ begin
     gem.add_dependency('modular-scale')
     #gem.add_dependency('zurb-foundation')
     gem.add_dependency('compass')
+    gem.add_dependency('sassc')
     gem.add_dependency('json')
     gem.add_dependency('haml')
     gem.add_dependency('rest-client')

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

@@ -77,7 +77,8 @@ module RbbtRESTHelpers
   #{{{ SASS
   
   def self.add_sass_load_path(path)
-    Sass::Engine::DEFAULT_OPTIONS[:load_paths].unshift path
+    sass_resources.unshift path
+    sass_resources.uniq!
   end
  
   def self.sass_resources

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

@@ -112,8 +112,8 @@ module RbbtRESTHelpers
   end
 
   def render_sass(file)
-    renderer = Sass::Engine.new(Open.read(file), :filename => file, 
-                                :style => production? ? :compressed : nil, 
+    renderer = SassC::Engine.new(Open.read(file), :filename => file, :syntax => :sass,
+                                :style => production? ? :compressed : :nested, :include_paths => RbbtRESTHelpers.sass_resources * ":",
                                 :debug_info => development? ? true : false)
     renderer.render
   end

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

@@ -1,4 +1,4 @@
-require 'sass'
+require 'sassc'
 require 'uglifier'
 
 module RbbtRESTHelpers

data/lib/rbbt/rest/entity.rb

@@ -358,7 +358,8 @@ module Sinatra
             file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
 
             content_type "application/json"
-            halt 200, TSV.open(file).to_json
+            tsv = TSV.open(file)
+            halt 200, tsv.to_json
           else
             map = Entity::Map.load_map(entity_type.split(":").first, column, map_id, user)
             raise "Map not found: #{ map_id }" if map.nil?

data/lib/rbbt/rest/helpers.rb

@@ -5,7 +5,7 @@ module Sinatra
       mime = nil
       Open.open(path) do |io|
         begin
-          mime = MimeMagic.by_path(io) 
+          mime = MimeMagic.by_path(path) 
           if mime.nil?
             io.rewind
             mime = MimeMagic.by_magic(io) 

data/lib/rbbt/rest/main.rb

@@ -39,7 +39,7 @@ module Sinatra
 
     def add_sass_load_path(path)
       path = path.find if Path === path
-      Sass::Engine::DEFAULT_OPTIONS[:load_paths].unshift path if File.exists? path
+      RbbtRESTHelpers.add_sass_load_path(path)
     end
 
     def self.registered(base)

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

@@ -151,8 +151,10 @@ module WorkflowRESTHelpers
       if job.path
         if Open.remote? job.path
           Open.open(job.path, :nocache => true)
-        else
+        elsif File.exists? job.path
           send_file(job.path)
+        else
+          halt 200, job.load
         end
       else
         halt(200, job.load.to_s)

data/share/views/compass/app.sass

@@ -1,4 +1,5 @@
-@import 'compass/css3/animation'
+//@import 'compass/css3/animation'
+@import 'mixins'
 @import 'screen_sizes'
 @import 'layout'
 @import 'card_templates'

data/share/views/compass/mixins.sass

@@ -0,0 +1,16 @@
+=animation-duration($sec)
+  animation-duration: $sec
+
+=keyframes($name)
+  @keyframes #{$name}
+    @content
+
+=box-shadow($color)
+  box-shadow: $color
+
+=opacity($amount)
+  opacity: $amount
+
+=animation($animation...)
+  animation: $animation
+

data/share/views/compass/tab_menu.sass

@@ -1,8 +1,7 @@
-
-
-@import "compass/css3/animation"
-@import "compass/css3/opacity"
-@import "compass/css3/box-shadow"
+@import "mixins"
+//@import "compass/css3/animation"
+//@import "compass/css3/opacity"
+//@import "compass/css3/box-shadow"
 
 $jiffy: 0.28s
 $jiffy: 0.14s

data/share/views/entity_partials/entity_map_card.haml

@@ -21,7 +21,7 @@
               %input(type='submit')
 
           - if (%w(pvalue p.value p-value pvalues p.values p-values qvalue q.value q-value qvalues q.values q-values) & map.fields.first.downcase.split(/\s+/)).any? and map.fields.first.downcase !~ /score$/
-            - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
+            - url = add_GET_param(@uri, '_format', 'pvalue_score')
             %a.ui.small.button(href=url) Pvalue score
 
             = reveal "QQ-plot", nil, :class => 'ui small button plot' do
@@ -56,16 +56,16 @@
 
           - if Gene == Entity.formats[map.key_field]
             - if map.key_field != "Ensembl Gene ID"
-              - url = add_GET_param(@fullpath, '_format', 'ensembl')
+              - url = add_GET_param(@uri, '_format', 'ensembl')
               %a.ensembl.ui.small.button(href=url) Ensembl
             - if map.key_field != "Associated Gene Name"
-              - url = add_GET_param(@fullpath, '_format', 'name')
+              - url = add_GET_param(@uri, '_format', 'name')
               %a.name.ui.small.button(href=url) Name
           - if "Rank" == map.fields.first
-            - url = add_GET_param(@fullpath, '_format', 'invert_ranks')
+            - url = add_GET_param(@uri, '_format', 'invert_ranks')
             %a.invert_ranks.ui.small.button(href=url) Invert ranks
           - else
-            - url = add_GET_param(@fullpath, '_format', 'ranks')
+            - url = add_GET_param(@uri, '_format', 'ranks')
             %a.ranks.ui.small.button(href=url) Ranks
           - if NumericValue == Entity.formats[map.fields.first] or (map.entity_templates[map.fields.first] and map.entity_templates[map.fields.first].annotation_types.include? NumericValue)
             - $page_entity_base_type = page_entity_base_type 

data/share/views/form.haml

@@ -15,7 +15,7 @@
           #{task_info[:description]}
 
   .form.action_parameters.ui.segment
-    = partial_render('partials/form', :id => id, :action => action, :method => 'post', 
+    = partial_render('partials/form', :id => id, :action => action, :method => 'post', :bundle => true,
       :enctype => "multipart/form-data", :info => task_info, :klass => 'workflow_task', :locals => locals)
 
   - if workflow.libdir.examples[task.to_s].exists?

data/share/views/partials/form.haml

@@ -5,6 +5,7 @@
 - enctype = 'multipart/form-data' unless defined? enctype
 - info    = {} unless defined? info
 - locals  = {} unless defined? locals
+- bundle  = false unless defined? bundle
 
 - klass = "#{klass} custom"
 
@@ -70,7 +71,7 @@
       !~ form_input(input, types[input], defaults[input], values[input] || locals[input], description, input_id, input_options)
 
 
-  - if inputs.any?
+  - if bundle && inputs.any?
     .bundle.ui.very.basic.segment.field
       Input file bundle in tar.gz (overrides page inputs)
       %input(type='file' name='__input_file_bundle' id='SINTEF_ROC__input_file_bundle')

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

@@ -5,7 +5,7 @@ rbbt.Job = function(workflow, task, inputs){
   this.inputs = inputs
 
   this.jobname = m.prop()
-  this.jobURL = function(){ return '/' + workflow + '/' + task + '/' + this.jobname() }
+  this.jobURL = function(){ return rbbt.url_add_script_name('/' + workflow + '/' + task + '/' + this.jobname()) }
   this.result = m.prop()
   this.info = m.prop()
 
@@ -52,7 +52,7 @@ rbbt.Job = function(workflow, task, inputs){
   this.exec = function(json){
     var deferred = m.deferred()
     
-    var url = '/' + workflow + '/' + task
+    var url = rbbt.url_add_script_name('/' + workflow + '/' + task)
 
     var data = new FormData()
     data.append("_cache_type", 'exec')
@@ -89,7 +89,7 @@ rbbt.Job = function(workflow, task, inputs){
       return deferred.promise
     }
 
-    var url = '/' + workflow + '/' + task
+    var url = rbbt.url_add_script_name('/' + workflow + '/' + task)
 
     var data = new FormData()
     data.append("_format", 'jobname')

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

@@ -1,12 +1,14 @@
 function list_entities(type, id){
   var url = "/entity_list" + '/' + type + '/' + id;
 
+  url = rbbt.url_add_script_name(url)
   return get_ajax({url: url, async: false, method: "GET", data: {_format: 'json'}})['entities']
 }
 
 function list_info(type, id){
   var url = "/entity_list" + '/' + type + '/' + id;
 
+  url = rbbt.url_add_script_name(url)
   return get_ajax({url: url, async: false, method: "GET", data: {_format: 'info'}})
 }
 
@@ -95,6 +97,7 @@ body.on('click', 'ul.new_list > li > a', function(){
   var entity_type = $(this).html();
   var url = '/entity_list/' + entity_type + '/new/'
 
+  url = rbbt.url_add_script_name(url)
   get_ajax({url: url, async: false}, function(data){$('#modal').modal('show', data, "New " + entity_type + " list"); $('#top_menu li.favourites').favourites('close')})
 
   

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

@@ -1,6 +1,8 @@
 function entity_map(type, column, id, complete){
   var url = "/entity_map" + '/' + clean_element(type) + '/' + clean_element(column) + '/' + clean_element(id);
-  return rbbt.ajax({url: url, async: false, method: "GET", data: {_format: 'json'}}, complete)
+  url = rbbt.url_add_script_name(url)
+  console.log( url)
+  return rbbt.ajax({url: url, async: false, method: "GET", data: {_format: 'json'}, complete: complete})
 }
 
 $('body').on('click', '#modal form.rename_map input[type=submit]', function(){
@@ -14,6 +16,7 @@ $('body').on('click', '#modal form.rename_map input[type=submit]', function(){
   var entity_type = map.type
   var column = map.column
   url = '/entity_map/rename/'+ clean_element(entity_type) + '/'+ clean_element(column) +'/' + clean_element(map_id) + '?new_name=' + clean_element(new_name)
+  url = rbbt.url_add_script_name(url)
   window.location = url
   return false
 })
@@ -29,6 +32,7 @@ $('body').on('click', '.rank_products form input[type=submit]', function(){
   var column = map.column
   var column2 = select.find('option:selected').attr('attr-column')
   url = "/entity_map/rank_products?map1=" + clean_element(map1) + "&map2=" + clean_element(map2) + '&entity_type=' + entity_type + "&column=" + column +  "&column2=" + column2
+  url = rbbt.url_add_script_name(url)
   window.location = url
   return false
 })

data/share/views/tasks.haml

@@ -1,5 +1,5 @@
 .workflow.tasks
-  %h3= workflow.to_s
+  %h1= workflow.to_s
 
   - unless workflow.documentation[:title].empty?
     :markdown 
@@ -9,7 +9,7 @@
       #{workflow.documentation[:description]}
 
 
-  %h5 Tasks
+  %h3 Tasks
 
   - unless workflow.documentation[:task_description].empty?
     :markdown 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.99
+  version: 1.8.100
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-21 00:00:00.000000000 Z
+date: 2018-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -66,6 +66,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: sassc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
@@ -205,6 +219,7 @@ files:
 - share/views/compass/documentation.sass
 - share/views/compass/layout.sass
 - share/views/compass/misc.sass
+- share/views/compass/mixins.sass
 - share/views/compass/screen_sizes.sass
 - share/views/compass/tab_menu.sass
 - share/views/documented_section.haml