rbbt-rest 1.8.70 → 1.8.71

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 37203fb12b55688a0dc482a5fce2a959564eb3a5
-  data.tar.gz: 7ff95ac1408fb6ab04a7279c6cc76e7da77763a8
+  metadata.gz: f8414a3fe54af9c718109a0d9721eeaa9e2ba4a5
+  data.tar.gz: ddb1b9f145f9609c7334830c933668c3b7ba8833
 SHA512:
-  metadata.gz: def03043d2f6e6dc0b46edf58999ebfdc21b6b60ea9432f8a0d36b506617ebbbef911abdc2c1b33f6aa497c9cf5f29356a66870eeb27d2c78043c4e4cf81a61b
-  data.tar.gz: 71828f7002a3ebc0a0a459567552bedd6ac46a4851696fba6a7c96cd9480d3aa8d307cfba2c1f8b44c4b799abb49228eec5a155faabc1f344802e4f3d64798bf
+  metadata.gz: 85b6145e42a9c0a61fc4f28174e187fd86fc087910febabfbd7230e2d5e1815cde612b8f7626458b4f77e3f33aa732069d2d2aade68b281e9297fc2d06f10c94
+  data.tar.gz: b2c14d4eb9dcf749a11ec1216b1cb33c1e2099358ff7516891501d82cc2fc93ff94921e428e647fcc96db522a3d2cd00c760add2cdff26a83e8a568ce3d72540

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

@@ -23,6 +23,13 @@ module RbbtRESTHelpers
     html_tag("textarea", value || "" , :name => name, :id => id )
   end
 
+  def tar_file(id, name, value)
+    tar_msg = "File in tar.gz format with directory as only first level entry"
+
+    html_tag("input", nil, :type => "file", :id => (id.nil? ? nil : id +  "__" + "param_file"), :name => name.to_s + "__" + "param_file") + 
+    html_tag("span", tar_msg, :class => "file_or_text_area")
+  end
+
   def form_input(name, type, default = nil, current = nil, description = nil, id = nil, extra = {})
     html_options = consume_parameter(:html_options, extra) || {}
 
@@ -138,8 +145,13 @@ module RbbtRESTHelpers
 
       input_label(id, name, description, default, extra) +
         html_tag('select', options * "\n", html_options.merge(:name => name, :id => id, "attr-selected" => (value ? value.to_s : "")))
+    when :directory
+      value = current.nil? ? default : current
+
+      input_label(id, name, description, nil, extra) +
+        tar_file(id, name, value)
     else
-      "<span> Unsupported input #{name} #{type} </span>"
+      "<span> Unsupported input '#{name}' type: #{type} </span>"
     end
   end
 end

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

@@ -216,6 +216,9 @@ module RbbtRESTHelpers
       else
         TSV.open(StringIO.new(value), :sep=>/\t|,/)
       end
+    when :directory
+      param_file[:tempfile].close
+      Path.setup(param_file[:tempfile].path)
     end
   end
 

data/lib/rbbt/rest/main.rb

@@ -76,7 +76,8 @@ module Sinatra
 
         before do
           method = request.request_method
-          request.script_name = request.env["HTTP_SCRIPT_NAME"]
+          $script_name = request.script_name = request.env["HTTP_SCRIPT_NAME"]
+
           method_color = case method
                          when "GET"
                            :cyan

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

@@ -231,7 +231,7 @@ module WorkflowRESTHelpers
         if format == :jobname
           job.name
         else
-          job_url = job.respond_to?(:url)? job.url : to(File.join("/", workflow.to_s, task, job.name)) 
+          job_url = job.respond_to?(:url)? job.url : File.join("/", workflow.to_s, task, job.name)
           job_url += "?_format=#{@format}" if @format
           redirect job_url
         end
@@ -254,7 +254,7 @@ module WorkflowRESTHelpers
           job.name
         else
           job.soft_grace
-          job_url = job.respond_to?(:url)? job.url : to(File.join("/", workflow.to_s, task, job.name)) 
+          job_url = job.respond_to?(:url)? job.url : File.join("/", workflow.to_s, task, job.name)
           job_url += "?_format=#{@format}" if @format
           redirect job_url
         end

data/share/views/compass/app.sass

@@ -15,7 +15,8 @@ a.entity
   text-overflow: ellipsis
   vertical-align: bottom
 
-.description
+.description.very.basic
+  padding: 2px !important
   overflow: hidden
   &:hover
     overflow: visible

data/share/views/layout/coda.haml

@@ -1,6 +1,8 @@
 = serve_js
 
 :javascript
+  var script_name = #{$script_name ? "'" + $script_name + "'"  : "undefined"}
+
   $('.offcanvas').click(function(e){ 
     if( e.target !== this ) 
       return;
@@ -11,36 +13,6 @@
 
   var known_types = #{Entity::REST::REST_ENTITIES.collect{|m| m.to_s}.to_json}
 
--#
-  function gene_name(name){
-    return new Entity({type: "Gene", id: name, name: name, format: "Associated Gene Name", info: { organism: "Hsa/feb2014" }})
-  }
-
-  function entity_link(entity){
-    return m('a', {href: entity.url()}, entity.name)
-  }
-
-  function entity_item(entity){
-    return m('li', entity_link(entity))
-  }
-
-  function entity_list(list){
-    return m('ul.entity_list', list.map(entity_item))
-  }
-
-  function draw_entity_list(list){
-    var content_elem = $('#content')[0]
-    var content = [m("p", {style: 'padding: 3em'}, entity_list(list))]
-    return m.render(content_elem, content)
-  }
-
-  function debug(name){
-    gene = gene_name(name)
-    gene.children("tfacts@genomics").then(draw_entity_list)
-    gene.parents("tfacts@genomics").then(draw_entity_list)
-  }
-
-
 - if @reload_page 
   :javascript
     var wait_timeout = 2000;

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

@@ -13,6 +13,13 @@ rbbt.ajax = function(params){
     params.config = function(xhr, options){ xhr.setRequestHeader( "X-Requested-With", "XMLHttpRequest"); return xhr; }
   }
 
+  console.log("AJAX")
+  console.log(params.url)
+  if (script_name != undefined && params.url[0] == "/" && params.url.indexOf(script_name) != 0){
+    params.url = script_name + params.url
+  }
+  console.log(params.url)
+
   if (params.cookies){
     var config = params.config
     if (undefined === config){ 

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

@@ -80,6 +80,6 @@ FavouriteEntities.deserialize = function(data){
 } 
 
 FavouriteEntities.get = function(){
-  return m.request({method: 'GET', url: '/favourite_entities', type: FavouriteEntities, deserialize: FavouriteEntities.deserialize})
+  return rbbt.ajax({method: 'GET', url: '/favourite_entities', type: FavouriteEntities, deserialize: FavouriteEntities.deserialize})
 }
 

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

@@ -82,7 +82,7 @@ var EntityList = function(data){
       var url = this.url()
       url = add_parameter(url, '_format', 'json')
       list = this
-      this.loading = m.request({url: url, method: 'GET'}).then(this.entities).then(function(x){ list.loading = undefined; return x})
+      this.loading = rbbt.ajax({url: url, method: 'GET'}).then(this.entities).then(function(x){ list.loading = undefined; return x})
       return this.loading
     }else{
       var deferred = m.deferred()
@@ -151,7 +151,7 @@ var FavouriteLists = function(by_type){
 }
 
 FavouriteLists.get = function(){
-  return m.request({method: 'GET', url: '/favourite_entity_lists', type: FavouriteLists, deserialize: FavouriteLists.deserialize})
+  return rbbt.ajax({method: 'GET', url: '/favourite_entity_lists', type: FavouriteLists, deserialize: FavouriteLists.deserialize})
 }
 
 FavouriteLists.deserialize = function(data){

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

@@ -16,7 +16,7 @@ var EntityMap = function(data){
  this.get = function(){ 
   var url = this.url()
   url = add_parameter(url, '_format', 'json')
-  return m.request({url: url, method: 'GET'})
+  return rbbt.ajax({url: url, method: 'GET'})
  }
 }
 
@@ -27,7 +27,7 @@ var FavouriteMaps = function(by_type){
 }
 
 FavouriteMaps.get = function(){
-  return m.request({method: 'GET', url: '/favourite_entity_maps', type: FavouriteMaps, deserialize: FavouriteMaps.deserialize})
+  return rbbt.ajax({method: 'GET', url: '/favourite_entity_maps', type: FavouriteMaps, deserialize: FavouriteMaps.deserialize})
 }
 
 FavouriteMaps.deserialize = function(data){

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.70
+  version: 1.8.71
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-09-21 00:00:00.000000000 Z
+date: 2017-09-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake