diff --git a/.yardoc/checksums b/.yardoc/checksums index 2868505..733e89f 100644 --- a/.yardoc/checksums +++ b/.yardoc/checksums @@ -1,4 +1,4 @@ -lib/classyfire_api.rb 4e5cc4102771d77c67759b9298ae685f0cb612cd +lib/classyfire_api.rb 3449cdc9aef5fb255b1fdc933f7d7653bb1fa960 lib/query_resource.rb 645cfb1688a5c44e67e5227fc0e9a77589731f24 lib/entity_resource.rb 6c50b4be6a5eb13b44d7080b19c7033b7a37c7cf lib/sequence_resource.rb d8c5007781d50d0bc13cbe360b617e2937a19428 diff --git a/.yardoc/objects/root.dat b/.yardoc/objects/root.dat index cf147b6..45e47d8 100644 Binary files a/.yardoc/objects/root.dat and b/.yardoc/objects/root.dat differ diff --git a/doc/ClassyFireAPI.html b/doc/ClassyFireAPI.html index fb1207f..5ba7df4 100644 --- a/doc/ClassyFireAPI.html +++ b/doc/ClassyFireAPI.html @@ -327,7 +327,7 @@ of a given size.

-

Submits a ClassyFire query, which should be returned in a specific format.

+

Submits a ClassyFire query in a JSON format.

 @@ -475,7 +475,6 @@ specified format.

 
 
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@@ -494,10 +493,11 @@ specified format.

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+80 +81 - 
# File 'lib/classyfire_api.rb', line 61
+      
# File 'lib/classyfire_api.rb', line 62
 
 def ClassyFireAPI.get_entity_classification(inchikey,format="json")
   inchikey_id = inchikey.to_s.gsub('InChIKey=','')
@@ -608,7 +608,6 @@ specified format.

       
 
 
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@@ -626,10 +625,11 @@ specified format.

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-      
# File 'lib/classyfire_api.rb', line 36
+      
# File 'lib/classyfire_api.rb', line 37
 
 def ClassyFireAPI.get_query(query_id,format="json")
   begin
@@ -739,7 +739,6 @@ specified format.

       
 
 
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-      
# File 'lib/classyfire_api.rb', line 87
+      
# File 'lib/classyfire_api.rb', line 88
 
 def ClassyFireAPI.get_sequence_classification(fingerprint,format="json")
   begin
@@ -842,17 +842,17 @@ specified format.

       
 
 
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-      
# File 'lib/classyfire_api.rb', line 128
+      
# File 'lib/classyfire_api.rb', line 129
 
 def ClassyFireAPI.query_status(query_id)
   begin
@@ -932,8 +932,6 @@ retrieve the strutcure's classification from ClassyFire.

       
 
 
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@@ -994,10 +992,12 @@ retrieve the strutcure's classification from ClassyFire.

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-      
# File 'lib/classyfire_api.rb', line 309
+      
# File 'lib/classyfire_api.rb', line 311
 
 def ClassyFireAPI.retrieve_classification(input,output)
   absolute_path = File.expand_path(input)
@@ -1133,8 +1133,6 @@ format.

       
 
 
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@@ -1186,10 +1184,12 @@ format.

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+431
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-      
# File 'lib/classyfire_api.rb', line 378
+      
# File 'lib/classyfire_api.rb', line 380
 
 def ClassyFireAPI.retrieve_entities_json(input,output)
   absolute_path = File.expand_path(input)
@@ -1316,8 +1316,6 @@ format.

       
 
 
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@@ -1375,10 +1373,12 @@ format.

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+499
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-      
# File 'lib/classyfire_api.rb', line 440
+      
# File 'lib/classyfire_api.rb', line 442
 
 def ClassyFireAPI.retrieve_entities_sdf(input,output)
   absolute_path = File.expand_path(input)
@@ -1509,8 +1509,6 @@ slice_length [Integer] The maximum number of entries for each query input
       
 
 
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@@ -1518,10 +1516,12 @@ slice_length [Integer] The maximum number of entries for each query input
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-      
# File 'lib/classyfire_api.rb', line 227
+      
# File 'lib/classyfire_api.rb', line 229
 
 def ClassyFireAPI.submit_queries_from_directory(folder,slice_length,type="STRUCTURE")
   if File.directory?(folder)
@@ -1550,7 +1550,7 @@ slice_length [Integer] The maximum number of entries for each query input
 

   

     
-
Submits a ClassyFire query, which should be returned in a specific format.

+
Submits a ClassyFire query in a JSON format.

 
 
if there is an error.

 
@@ -1589,6 +1589,24 @@ slice_length [Integer] The maximum number of entries for each query input
         —
         

 
the input of the query.

+

+      
+    
+  
+    
  • 
+      
+        type
+      
+      
+        (String)
+      
+      
+        (defaults to: 'STRUCTURE')
+      
+      
+        —
+        
    
+
    the type of the query.
    
 
    
       
     
    • 
@@ -1620,7 +1638,6 @@ slice_length [Integer] The maximum number of entries for each query input
       
     
 
-13
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@@ -1635,10 +1652,11 @@ slice_length [Integer] The maximum number of entries for each query input
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-      
    # File 'lib/classyfire_api.rb', line 13
+      
    # File 'lib/classyfire_api.rb', line 14
 
 def ClassyFireAPI.submit_query(label,input, type='STRUCTURE')
   begin
@@ -1722,7 +1740,6 @@ framgments from the index 'start'.
    
       
     
 
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@@ -1784,10 +1801,12 @@ framgments from the index 'start'.
    
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+212
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-      
    # File 'lib/classyfire_api.rb', line 150
+      
    # File 'lib/classyfire_api.rb', line 151
 
 def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length, start, type='STRUCTURE')
   @start_time = Time.now
@@ -1802,7 +1821,7 @@ framgments from the index 'start'.
    
     if sline.length == 1
       input <<"#{sline[0]}"
     elsif sline.length >= 2
-      input <<"#{sline[0]}\t#{sline[2]}"
+      input <<"#{sline[0]}\t#{sline[1]}"
     end
   end
 
@@ -1817,15 +1836,17 @@ framgments from the index 'start'.
    
   while i <  initial_nr_of_jobs
     title     = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"
 
-    begin
-      puts "submitting #{title}"
-      q       = submit_query(title,subdivised_groups[i-1].join("\n"),type)
-      query_ids << JSON.parse(q)['id']
-    rescue Exception => e  
-      puts e.message  
-      puts e.backtrace.inspect
+    if i <= subdivised_groups.length
+      begin
+        puts "submitting #{title}"
+        q       = submit_query(title,subdivised_groups[i-1].join("\n"),type)
+        query_ids << JSON.parse(q)['id']
+      rescue Exception => e  
+        puts e.message  
+        puts e.backtrace.inspect
+      end
+      i = i + 1
     end
-    i = i + 1
   end
 
   puts "Going to sleep at #{Time.now - @start_time} for #{sleeping_time} s."
@@ -1844,7 +1865,6 @@ framgments from the index 'start'.
    
         puts e.message  
         puts e.backtrace.inspect
       end
-      
     end
     i = k
     puts "Going to sleep at #{Time.now - @start_time} for #{sleeping_time} s."
@@ -1950,8 +1970,6 @@ text. is fragmented into n part of #slice_length entries each).
    
       
     
 
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@@ -2000,10 +2018,12 @@ text. is fragmented into n part of #slice_length entries each).
    
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+302
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-      
    # File 'lib/classyfire_api.rb', line 252
+      
    # File 'lib/classyfire_api.rb', line 254
 
 def ClassyFireAPI.submit_random_subset_of_query_input_in_chunks(tab_separated_input_file,size, type='STRUCTURE')
   @start_time = Time.now
@@ -2066,7 +2086,7 @@ text. is fragmented into n part of #slice_length entries each).
    
 
 
     
diff --git a/doc/EntityResource.html b/doc/EntityResource.html
index 751e75d..a5202f3 100644
--- a/doc/EntityResource.html
+++ b/doc/EntityResource.html
@@ -114,7 +114,7 @@
 
 
     
diff --git a/doc/QueryResource.html b/doc/QueryResource.html
index 0bad01d..6538bb0 100644
--- a/doc/QueryResource.html
+++ b/doc/QueryResource.html
@@ -183,7 +183,7 @@
 
 
     
diff --git a/doc/SequenceResource.html b/doc/SequenceResource.html
index 25cf179..c1c1a8e 100644
--- a/doc/SequenceResource.html
+++ b/doc/SequenceResource.html
@@ -114,7 +114,7 @@
 
 
     
diff --git a/doc/_index.html b/doc/_index.html
index 75f45b6..64f3f27 100644
--- a/doc/_index.html
+++ b/doc/_index.html
@@ -140,7 +140,7 @@
 
 
     
diff --git a/doc/file.README.html b/doc/file.README.html
index e3f7fc1..c669d32 100644
--- a/doc/file.README.html
+++ b/doc/file.README.html
@@ -236,7 +236,7 @@ XML format.
    
 
 
     
diff --git a/doc/index.html b/doc/index.html
index e3f7fc1..c669d32 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -236,7 +236,7 @@ XML format.
    
 
 
     
diff --git a/doc/top-level-namespace.html b/doc/top-level-namespace.html
index 6cb613a..5468c69 100644
--- a/doc/top-level-namespace.html
+++ b/doc/top-level-namespace.html
@@ -105,7 +105,7 @@
 
 
     
diff --git a/lib/classyfire_api.rb b/lib/classyfire_api.rb
index 7c5e780..2c16c24 100644
--- a/lib/classyfire_api.rb
+++ b/lib/classyfire_api.rb
@@ -4,10 +4,11 @@ require 'csv'
 module ClassyFireAPI
   URL = 'http://classyfire.wishartlab.com'
 
-  # Submits a ClassyFire query, which should be returned in a specific format.
+  # Submits a ClassyFire query in a JSON format.
   #
   # @param label [String] the label of the query.
-  # @param input[String] the input of the query.
+  # @param input [String] the input of the query.
+  # @param type [String] the type of the query.
   # @return [Hash] A Ruby Hash with the id (and other attributes) of the Query or nil
   # if there is an error.
   def ClassyFireAPI.submit_query(label,input, type='STRUCTURE')
@@ -160,7 +161,7 @@ module ClassyFireAPI
       if sline.length == 1
         input <<"#{sline[0]}"
       elsif sline.length >= 2
-        input <<"#{sline[0]}\t#{sline[2]}"
+        input <<"#{sline[0]}\t#{sline[1]}"
       end
     end