rbbt-views 2.0.0 → 2.0.1

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

@@ -27,6 +27,10 @@ class RbbtRestClient
           attr_accessor :remote_name
           attr_accessor :original_name
           attr_accessor :remote_export
+
+          def remote_name
+            URI.escape(@remote_name)
+          end
         end
 
         step.original_name = name || "RestClient"
@@ -49,13 +53,13 @@ class RbbtRestClient
           def load
             case task.result_type.to_sym
             when :string
-              RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=raw")
+              RestClient.get(File.join(task.url, task.name.to_s, remote_name) + "?_format=raw")
             when :tsv
-              TSV.open(StringIO.new(RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=raw")))
+              TSV.open(StringIO.new(RestClient.get(File.join(task.url, task.name.to_s, remote_name) + "?_format=raw")))
             when :annotations
-              Annotated.load_tsv(TSV.open(StringIO.new(RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=raw"))))
+              Annotated.load_tsv(TSV.open(StringIO.new(RestClient.get(File.join(task.url, task.name.to_s, remote_name) + "?_format=raw"))))
             else
-              res = JSON.parse(RestClient.get(File.join(task.url, task.name.to_s, @remote_name) + "?_format=json"))
+              res = JSON.parse(RestClient.get(File.join(task.url, task.name.to_s, remote_name) + "?_format=json"))
               res = TSV.setup(res) if task.result_type.to_sym == :tsv
               res
             end
@@ -63,27 +67,22 @@ class RbbtRestClient
 
           def exec
             input_hash = Misc.zip2hash(task.inputs, @inputs)
-            input_str = input_hash.collect{|k,v| 
-              [k, 
-                Array === v ? v.dup.collect{|vv| CGI.escape(vv.to_s)} * "," : CGI.escape(v.to_s)
-              ] * "="
-            } * "&"
 
             case remote_export.to_s 
             when "exec"
               url = File.join(task.url, task.name.to_s)
               if task.result_type.to_sym == :string
-                res = RestClient.post(url, input_hash.merge(:_format => :raw))
+                res = RestClient.post(url, Misc.hash2GET_params(input_hash.merge(:_format => :raw)))
                 res
               else
-                res = RestClient.post(url, input_hash.merge(:_format => :json))
+                res = RestClient.post(url, Misc.hash2GET_params(input_hash.merge(:_format => :json)))
                 JSON.parse(res)
               end
             when "synchronous"
-              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), input_hash.merge(:_format => :json, :jobname => original_name))
+              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), Misc.hash2GET_params(input_hash.merge(:_format => :json, :jobname => original_name)))
               self.load
             when "asynchronous"
-              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), input_hash.merge(:_format => :json, :jobname => original_name))
+              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), Misc.hash2GET_params(input_hash.merge(:_format => :json, :jobname => original_name)))
               while not done?
                 sleep 10
               end
@@ -97,16 +96,15 @@ class RbbtRestClient
 
           def fork
             input_hash = Misc.zip2hash(task.inputs, @inputs)
-            input_str = input_hash.collect{|p| p * "="} * "&"
 
             case remote_export.to_s 
             when "exec"
               raise "Cannot export a remote function exported as 'exec'"
             when "synchronous"
-              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), input_hash.merge(:_format => :json, :jobname =>  original_name))
+              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), Misc.hash2GET_params(input_hash.merge(:_format => :json, :jobname =>  original_name)))
               self
             when "asynchronous"
-              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), input_hash.merge(:_format => :json, :jobname =>  original_name))
+              @remote_name = RestClient.post(File.join(task.url, task.name.to_s), Misc.hash2GET_params(input_hash.merge(:_format => :json, :jobname =>  original_name)))
               self
             end
           end

data/test/rbbt/workflow/rest/test_client.rb

@@ -3,8 +3,17 @@ require 'rbbt/workflow/rest/client'
 
 class TestRestClient < Test::Unit::TestCase
 
+  def test_name_escape
+    driver = RbbtRestClient.new 'http://studyexplorer.bioinfo.cnio.es/Sequence', "Sequence"
+    job = driver.job(:genes_at_genomic_positions, "Default (escape)", :organism => "Hsa", :positions => %w(1:123123:A))
+    assert_equal %w(ENSG00000238009), job.exec.values.flatten
+    assert_equal %w(ENSG00000238009), job.run.values.flatten
+    job.clean
+  end
+
+
   def test_client_exec
-    driver = RbbtRestClient.new 'http://localhost:1984/Sequence'
+    driver = RbbtRestClient.new 'http://studyexplorer.bioinfo.cnio.es/Sequence', "Sequence"
     job = driver.job(:genes_at_genomic_positions, "Default", :organism => "Hsa", :positions => %w(1:123123:A))
     assert_equal %w(ENSG00000238009), job.exec.values.flatten
     assert_equal %w(ENSG00000238009), job.run.values.flatten
@@ -12,7 +21,7 @@ class TestRestClient < Test::Unit::TestCase
   end
 
   def test_client_synchronous
-    driver = RbbtRestClient.new 'http://localhost:1984/Sequence'
+    driver = RbbtRestClient.new 'http://studyexplorer.bioinfo.cnio.es/Sequence', "Sequence"
     job = driver.job(:mutated_isoforms_for_genomic_mutations, "Default", :organism => "Hsa", :mutations => %w(9:140051238:G))
     assert job.exec.values.flatten.include? "ENSP00000316915:P263P"
     job.clean

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-views
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-21 00:00:00.000000000 Z
+date: 2013-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sinatra
@@ -995,15 +995,14 @@ files:
 - share/views/public/plugins/tablesorter/themes/green/green.zip
 - share/views/public/plugins/tablesorter/themes/green/style.css
 - share/views/public/plugins/wz_jsgraphics.js
-- share/views/public/tmp/foo
 - share/views/result.haml
 - share/views/step_error.haml
 - share/views/task_list.haml
 - share/views/user_lists.haml
 - share/views/wait.haml
 - LICENSE
-- test/test_helper.rb
 - test/rbbt/workflow/rest/test_client.rb
+- test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-views
 licenses: []
 post_install_message: 
@@ -1029,5 +1028,5 @@ signing_key:
 specification_version: 3
 summary: Rest and HTML interface
 test_files:
-- test/test_helper.rb
 - test/rbbt/workflow/rest/test_client.rb
+- test/test_helper.rb