rbbt-rest 1.8.100 → 1.8.101

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6e300de985d4e401a9ade4802219274d354e318b
-  data.tar.gz: 698553ac0867819d9ac1b63eebfa92111125adc0
+  metadata.gz: fc57d8156b2175378706469776115cc8394a8c56
+  data.tar.gz: c81bb2d8f99fecbc182b6e24079a18df9fed3764
 SHA512:
-  metadata.gz: bb8f336021a91d2fd6ca900416a147d272a054efeabdde75744e57f95609f305bd80ab08746b24b1a57e85b50fb316bfce1779216dc4ab0e2bbb28712059d06b
-  data.tar.gz: 897331ed434c75939f6fa368b61b66705f10566d28dafdf90fc9bae35ac6be2c3924300a8677653a9e76d8df39205bcf9cb08773e804d3d4084125962a6c2def
+  metadata.gz: 90cf4c082961fd9e7efe46307230355154d93e838a4124b80615ec8aedf2fa4d3948515bb4730769572b980d11292629a74748f4a6baacaaddd0b51a90ff067e
+  data.tar.gz: f3c03f11cd8a830e5226ecc43a38f653b1b8dfe8df3f527898c51ed838842737e9cb537de7df9dbd387ec7c52f2452ab6db3c76907bbab8cfdea0a50ab555bca

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

@@ -216,7 +216,11 @@ module RbbtRESTHelpers
     if filter and filter.to_s != "false"
       filter.split(";;").each do |f|
         key, value = f.split("~")
+        orig_key = key
+        format = Entity.formats.find(key)
+        type = Entity.formats[format] if format
         next if value.nil? or value.empty?
+
         value =  Entity::REST.restore_element(value)
 
         #invert
@@ -235,6 +239,7 @@ module RbbtRESTHelpers
           name = false
         end
 
+        #length
         if value =~ /^:length:\s*(.*)/
           value = $1
           length = true
@@ -261,6 +266,11 @@ module RbbtRESTHelpers
         end
         
         case
+        when value =~ /^(%in%)\s*(.*)/ 
+          raise "Entity type not recognized for field: #{orig_key}" if type.nil?
+          list_name = $2
+          list = Entity::List.load_list(type, list_name)
+          tsv = tsv.select(key, invert){|k| k = k.first if Array === k; (k.nil? or (String === k and k.empty?)) ? false : list.include?(k)}
         when value =~ /^([<>]=?)(.*)/
           tsv = tsv.select(key, invert){|k| k = k.first if Array === k; (k.nil? or (String === k and k.empty?)) ? false : k.to_f.send($1, $2.to_f)}
         when value =~ /^\/(.+)\/.{0,2}\s*$/
@@ -451,7 +461,7 @@ module RbbtRESTHelpers
       tsv, table_options = load_tsv(file)
     end
 
-    table_options[:heatmap] = tsv.cast && %w(to_i to_f).include?(tsv.cast.to_s) unless table_options.include? :heatmap
+    table_options[:heatmap] = (tsv.cast && %w(to_i to_f).include?(tsv.cast.to_s) && tsv.fields.length > 1) unless table_options.include? :heatmap
 
     table_options = default_table_options.merge(table_options)
 

data/lib/rbbt/rest/entity/list.rb

@@ -15,7 +15,7 @@ module Entity
       id = Entity::REST.clean_element(id)
       id = Misc.sanitize_filename(id)
 
-      entity_type = entity_type.split(":").first
+      entity_type = entity_type.to_s.split(":").first
 
       raise "Ilegal list id: #{ id }" unless Misc.path_relative_to Entity.entity_list_cache, File.join(Entity.entity_list_cache, id)
 

data/share/views/partials/table/filters.haml

@@ -19,6 +19,7 @@
       - *String of text*: perfect match (e.g. `'Cancer'`)
       - *Regular expression*: flexible match (e.g. `'/(bladder|breast)\s+cancer/i'`)
       - *Numeric comparison*: lower of grater than (e.g. `'< 0.1'` or `'>= 2'`)
+      - *In an Entity List*: for lists that match the entity implied by the header (e.g. '%in% \<list name\>')
       - *Names*: for entities having 'human-friendly' names, such as genes or pathways; regular expression accepted (e.g. `':name: SF3B1'` or `':name: /CDK\d/'`)
       - *Length*: for lists (e.g. `':length: > 2'`)
       - *Negation*: Any of the rules above can be negated by prepending the `!` character (e.g. `'!:name:/^IG/'`)

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

@@ -5,7 +5,10 @@ rbbt.mlog = function(data){
 
 // AJAX
 
-rbbt.ajax = function(params){
+rbbt.ajax = function(params, complete){
+  if (undefined === params.complete){
+   params.complete = complete
+  }
   if (undefined === params.method) params.method = "GET"
   if (rbbt.proxy && params.url.indexOf('//') < 0 && params.url.indexOf('/') == 0){
     params.url = rbbt.proxy + params.url
@@ -121,6 +124,9 @@ rbbt.get = function(url, params){
 
 rbbt.post = function(url, data, params){
   var request_params
+  if (typeof params === 'function'){
+    params = {complete: params}
+  }
   if (typeof url === 'object'){
     request_params = url
     if (data) request_params.data = data

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

@@ -63,3 +63,13 @@ rbbt.url_add_script_name = function(url){
 
   return url
 }
+
+rbbt.link_add_script_name = function(link){
+  
+  console.log(link)
+  var l = $(link)
+  console.log(l)
+  l.attr('href', rbbt.url_add_script_name(l.attr('href')))
+  return l[0].outerHTML;
+}
+

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

@@ -41,6 +41,7 @@ ModalComponent = function(element){
     }
 
     ctrl.show_url = function(url, title){
+      url = rbbt.url_add_script_name(url)
       if (typeof url == 'string') params = {url: url, method: 'GET',deserialize: function(v){return v}}
       else params = url
 

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

@@ -57,6 +57,8 @@ body.on('click', 'a.intersect_lists', function(){
   var list_id = rbbt.page.list().id;
   var params = "other_list_id=" + clean_element(other_list_id)
   var url = "/entity_list/intersect/" + clean_element(type) + "/" + clean_element(list_id) + "?" + params
+
+  url = rbbt.url_add_script_name(url)
   window.location= url
 })
 
@@ -67,6 +69,8 @@ body.on('click', 'a.remove_list', function(){
   var list_id = rbbt.page.list().id;
   var params = "other_list_id=" + clean_element(other_list_id)
   var url = "/entity_list/remove/" + clean_element(type) + "/" + clean_element(list_id) + "?" + params
+
+  url = rbbt.url_add_script_name(url)
   window.location= url
 })
 
@@ -77,6 +81,7 @@ body.on('click', 'a.add_list', function(){
   var list_id = rbbt.page.list().id;
   var params = "other_list_id=" + clean_element(other_list_id)
   var url = "/entity_list/add/" + clean_element(type) + "/" + clean_element(list_id) + "?" + params
+  url = rbbt.url_add_script_name(url)
   window.location= url
 })
 
@@ -87,6 +92,7 @@ body.on('click', 'a.edit_list', function(){
   var list_id = rbbt.page.list().id;
 
   var url = '/entity_list/' + clean_element(entity_type) + '/edit/' + clean_element(list_id)
+  url = rbbt.url_add_script_name(url)
 
   rbbt.modal.controller.show_url(url, "Edit list")
   
@@ -126,6 +132,7 @@ body.on('click', '.edit_list input[type=submit]', function(){
 
   var url = '/entity_list/' + clean_element(entity_type) + '/' + clean_element(new_list_id  )
 
+  url = rbbt.url_add_script_name(url)
   get_ajax({url: url, type: 'POST', async: false, data: {annotations: JSON.stringify(annotations), entities: entities}}, function(){ window.location = url })
 
   return false

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.100
+  version: 1.8.101
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-07 00:00:00.000000000 Z
+date: 2018-11-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake