- updated the documentation
- added onpenbabel gem (but still issues with need. (so users still need to download and install obabel)
This commit is contained in:
djoumbou
parent
e6a10deb22
commit
7b532839d9
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@ -1,4 +1,5 @@
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|||
lib/classyfire_api.rb 3449cdc9aef5fb255b1fdc933f7d7653bb1fa960
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||||
lib/node_resource.rb 91abffbffddd88d43c4fd5408272fa112e053b8d
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||||
lib/classyfire_api.rb af1ffb46316f8e1ef09996ab2ca92f19be33c444
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||||
lib/query_resource.rb 645cfb1688a5c44e67e5227fc0e9a77589731f24
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||||
lib/entity_resource.rb 6c50b4be6a5eb13b44d7080b19c7033b7a37c7cf
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lib/sequence_resource.rb d8c5007781d50d0bc13cbe360b617e2937a19428
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3
Gemfile
3
Gemfile
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@ -1,4 +1,7 @@
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|||
source "https://rubygems.org"
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#ruby-2.3.0-dev
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gem 'rest-client'
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gem 'yard'
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gem 'activeresource'
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gem 'openbabel'
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25
Gemfile.lock
25
Gemfile.lock
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@ -1,16 +1,39 @@
|
|||
GEM
|
||||
remote: https://rubygems.org/
|
||||
specs:
|
||||
activemodel (4.2.6)
|
||||
activesupport (= 4.2.6)
|
||||
builder (~> 3.1)
|
||||
activeresource (4.1.0)
|
||||
activemodel (~> 4.0)
|
||||
activesupport (~> 4.0)
|
||||
rails-observers (~> 0.1.2)
|
||||
activesupport (4.2.6)
|
||||
i18n (~> 0.7)
|
||||
json (~> 1.7, >= 1.7.7)
|
||||
minitest (~> 5.1)
|
||||
thread_safe (~> 0.3, >= 0.3.4)
|
||||
tzinfo (~> 1.1)
|
||||
builder (3.2.2)
|
||||
domain_name (0.5.20160309)
|
||||
unf (>= 0.0.5, < 1.0.0)
|
||||
http-cookie (1.0.2)
|
||||
domain_name (~> 0.5)
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||||
i18n (0.7.0)
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||||
json (1.8.3)
|
||||
mime-types (2.99.1)
|
||||
minitest (5.9.0)
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||||
netrc (0.11.0)
|
||||
openbabel (2.3.2.2)
|
||||
rails-observers (0.1.2)
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||||
activemodel (~> 4.0)
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||||
rest-client (1.8.0)
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||||
http-cookie (>= 1.0.2, < 2.0)
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||||
mime-types (>= 1.16, < 3.0)
|
||||
netrc (~> 0.7)
|
||||
thread_safe (0.3.5)
|
||||
tzinfo (1.2.2)
|
||||
thread_safe (~> 0.1)
|
||||
unf (0.1.4)
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||||
unf_ext
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||||
unf_ext (0.0.7.2)
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||||
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@ -20,6 +43,8 @@ PLATFORMS
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|||
ruby
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||||
DEPENDENCIES
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activeresource
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openbabel
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||||
rest-client
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||||
yard
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||||
|
||||
|
|
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|||
File diff suppressed because it is too large
Load Diff
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@ -114,9 +114,9 @@
|
|||
</div>
|
||||
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||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:59 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
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||||
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|||
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@ -0,0 +1,123 @@
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|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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||||
<title>
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||||
Class: NodeResource
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||||
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||||
— Documentation by YARD 0.8.7.6
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</title>
|
||||
|
||||
<link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
|
||||
|
||||
<link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
|
||||
|
||||
<script type="text/javascript" charset="utf-8">
|
||||
hasFrames = window.top.frames.main ? true : false;
|
||||
relpath = '';
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||||
framesUrl = "frames.html#!NodeResource.html";
|
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</script>
|
||||
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||||
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||||
<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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||||
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||||
<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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||||
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|
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</head>
|
||||
<body>
|
||||
<div id="header">
|
||||
<div id="menu">
|
||||
|
||||
<a href="_index.html">Index (N)</a> »
|
||||
|
||||
|
||||
<span class="title">NodeResource</span>
|
||||
|
||||
|
||||
<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
|
||||
</div>
|
||||
|
||||
<div id="search">
|
||||
|
||||
<a class="full_list_link" id="class_list_link"
|
||||
href="class_list.html">
|
||||
Class List
|
||||
</a>
|
||||
|
||||
<a class="full_list_link" id="method_list_link"
|
||||
href="method_list.html">
|
||||
Method List
|
||||
</a>
|
||||
|
||||
<a class="full_list_link" id="file_list_link"
|
||||
href="file_list.html">
|
||||
File List
|
||||
</a>
|
||||
|
||||
</div>
|
||||
<div class="clear"></div>
|
||||
</div>
|
||||
|
||||
<iframe id="search_frame"></iframe>
|
||||
|
||||
<div id="content"><h1>Class: NodeResource
|
||||
|
||||
|
||||
|
||||
</h1>
|
||||
|
||||
<dl class="box">
|
||||
|
||||
<dt class="r1">Inherits:</dt>
|
||||
<dd class="r1">
|
||||
<span class="inheritName">ActiveResource::Base</span>
|
||||
|
||||
<ul class="fullTree">
|
||||
<li>Object</li>
|
||||
|
||||
<li class="next">ActiveResource::Base</li>
|
||||
|
||||
<li class="next">NodeResource</li>
|
||||
|
||||
</ul>
|
||||
<a href="#" class="inheritanceTree">show all</a>
|
||||
|
||||
</dd>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<dt class="r2 last">Defined in:</dt>
|
||||
<dd class="r2 last">lib/node_resource.rb</dd>
|
||||
|
||||
</dl>
|
||||
<div class="clear"></div>
|
||||
|
||||
|
||||
|
||||
|
||||
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||||
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||||
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Tue Jun 28 15:46:59 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -183,9 +183,9 @@
|
|||
</div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:59 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -114,9 +114,9 @@
|
|||
</div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:59 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -106,6 +106,19 @@
|
|||
</ul>
|
||||
|
||||
|
||||
<ul id="alpha_N" class="alpha">
|
||||
<li class="letter">N</li>
|
||||
<ul>
|
||||
|
||||
<li>
|
||||
<span class='object_link'><a href="NodeResource.html" title="NodeResource (class)">NodeResource</a></span>
|
||||
|
||||
</li>
|
||||
|
||||
</ul>
|
||||
</ul>
|
||||
|
||||
|
||||
<ul id="alpha_Q" class="alpha">
|
||||
<li class="letter">Q</li>
|
||||
<ul>
|
||||
|
|
@ -140,9 +153,9 @@
|
|||
</div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:58 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@
|
|||
|
||||
<ul id="full_list" class="class">
|
||||
<li><span class='object_link'><a href="top-level-namespace.html" title="Top Level Namespace (root)">Top Level Namespace</a></span></li>
|
||||
<li><span class='object_link'><a href="ClassyFireAPI.html" title="ClassyFireAPI (module)">ClassyFireAPI</a></span><small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li>
|
||||
<li><span class='object_link'><a href="ClassyFireAPI.html" title="ClassyFireAPI (module)">ClassyFireAPI</a></span><small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="NodeResource.html" title="NodeResource (class)">NodeResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li><li><span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span> < Base<small class='search_info'>Top Level Namespace</small></li>
|
||||
|
||||
</ul>
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -236,9 +236,9 @@ XML format.</p>
|
|||
</div></div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:59 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -236,9 +236,9 @@ XML format.</p>
|
|||
</div></div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:58 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -52,67 +52,67 @@
|
|||
|
||||
|
||||
<li class="r1 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#get_chemont_node-class_method" title="ClassyFireAPI.get_chemont_node (method)">get_chemont_node</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r2 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#get_entity_classification-class_method" title="ClassyFireAPI.get_entity_classification (method)">get_entity_classification</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r2 ">
|
||||
<li class="r1 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#get_query-class_method" title="ClassyFireAPI.get_query (method)">get_query</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r1 ">
|
||||
<li class="r2 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#get_sequence_classification-class_method" title="ClassyFireAPI.get_sequence_classification (method)">get_sequence_classification</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r2 ">
|
||||
<li class="r1 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#query_status-class_method" title="ClassyFireAPI.query_status (method)">query_status</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r1 ">
|
||||
<li class="r2 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#retrieve_classification-class_method" title="ClassyFireAPI.retrieve_classification (method)">retrieve_classification</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r2 ">
|
||||
<li class="r1 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#retrieve_entities_json-class_method" title="ClassyFireAPI.retrieve_entities_json (method)">retrieve_entities_json</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r1 ">
|
||||
<li class="r2 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#retrieve_entities_sdf-class_method" title="ClassyFireAPI.retrieve_entities_sdf (method)">retrieve_entities_sdf</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r2 ">
|
||||
<li class="r1 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#submit_queries_from_directory-class_method" title="ClassyFireAPI.submit_queries_from_directory (method)">submit_queries_from_directory</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r1 ">
|
||||
<li class="r2 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#submit_query-class_method" title="ClassyFireAPI.submit_query (method)">submit_query</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r2 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#submit_query_input_in_chunks-class_method" title="ClassyFireAPI.submit_query_input_in_chunks (method)">submit_query_input_in_chunks</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
||||
<li class="r1 ">
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#submit_random_subset_of_query_input_in_chunks-class_method" title="ClassyFireAPI.submit_random_subset_of_query_input_in_chunks (method)">submit_random_subset_of_query_input_in_chunks</a></span>
|
||||
<span class='object_link'><a href="ClassyFireAPI.html#submit_query_input_in_chunks-class_method" title="ClassyFireAPI.submit_query_input_in_chunks (method)">submit_query_input_in_chunks</a></span>
|
||||
<small>ClassyFireAPI</small>
|
||||
</li>
|
||||
|
||||
|
|
|
|||
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|
@ -89,7 +89,7 @@
|
|||
|
||||
|
||||
|
||||
<strong class="classes">Classes:</strong> <span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span>, <span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span>, <span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span>
|
||||
<strong class="classes">Classes:</strong> <span class='object_link'><a href="EntityResource.html" title="EntityResource (class)">EntityResource</a></span>, <span class='object_link'><a href="NodeResource.html" title="NodeResource (class)">NodeResource</a></span>, <span class='object_link'><a href="QueryResource.html" title="QueryResource (class)">QueryResource</a></span>, <span class='object_link'><a href="SequenceResource.html" title="SequenceResource (class)">SequenceResource</a></span>
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||||
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||||
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||||
</p>
|
||||
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|
@ -105,9 +105,9 @@
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|||
</div>
|
||||
|
||||
<div id="footer">
|
||||
Generated on Thu Mar 10 15:54:06 2016 by
|
||||
Generated on Tue Jun 28 15:46:59 2016 by
|
||||
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
||||
0.8.7.6 (ruby-2.3.0).
|
||||
0.8.7.6 (ruby-2.4.0).
|
||||
</div>
|
||||
|
||||
</body>
|
||||
|
|
|
|||
|
|
@ -1,17 +1,18 @@
|
|||
require 'JSON'
|
||||
require 'csv'
|
||||
require 'rest-client'
|
||||
require 'openbabel'
|
||||
# require 'node_resource.rb'
|
||||
|
||||
module ClassyFireAPI
|
||||
URL = 'http://classyfire.wishartlab.com'
|
||||
|
||||
# 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 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.
|
||||
# if there is an error. Use JSON.parse to get a the json object.
|
||||
def ClassyFireAPI.submit_query(label,input, type='STRUCTURE')
|
||||
begin
|
||||
q = RestClient.post URL+'/queries', {:label => label, :query_input => input, :query_type => type}.to_json, :accept => :json, :content_type => :json
|
||||
|
|
@ -55,21 +56,15 @@ module ClassyFireAPI
|
|||
end
|
||||
end
|
||||
|
||||
# Retrieves the classification results for a given entity.
|
||||
# Return data for the TaxNode with ID chemontid.
|
||||
#
|
||||
# @param inchikey [String] the InChIKey of the entity.
|
||||
# @param format [String] the format of the query, 'text' (either JSON, CSV, or SDF)
|
||||
# @return [Text] A text file displaying the classification results for the entity in the specified format.
|
||||
def ClassyFireAPI.get_entity_classification(inchikey,format="json")
|
||||
# inchikey_id = inchikey.to_s.gsub('InChIKey=','')
|
||||
# @param chemontid [String] the ChemOnt ID of the entity.
|
||||
# @return [Text] A text displaying the classification results for the entity in the specified format.
|
||||
# Use JSON.parse to get a the json object.
|
||||
def ClassyFireAPI.get_chemont_node(chemontid)
|
||||
chemont_id = chemontid.to_s.gsub("CHEMONTID:","C")
|
||||
begin
|
||||
if format == "json"
|
||||
RestClient.get "#{URL}/entities/#{inchikey}.#{format}", :accept => :json
|
||||
elsif format == "sdf"
|
||||
RestClient.get "#{URL}/entities/#{inchikey}.#{format}", :accept => :sdf
|
||||
elsif format == "csv"
|
||||
RestClient.get "#{URL}/entities/#{inchikey}.#{format}", :accept => :csv
|
||||
end
|
||||
RestClient.get "#{URL}/tax_nodes/#{chemont_id}.json", :accept => :json
|
||||
rescue RestClient::ResourceNotFound => e
|
||||
e.response
|
||||
rescue RestClient::InternalServerError => e
|
||||
|
|
@ -83,9 +78,10 @@ module ClassyFireAPI
|
|||
|
||||
# Retrieves the classification results for a given sequence.
|
||||
#
|
||||
# @param the fingerprint [String] the fingerprint (generated from the sequence using Digest::MD5).
|
||||
# @param fingerprint [String] the fingerprint (generated from the sequence using Digest::MD5).
|
||||
# @param format [String] the format of the query (Only JSON)
|
||||
# @return [Text] A text file displaying the classification results for the entity in the specified format.
|
||||
# @return [Text] A text displaying the classification results for the entity in the specified format.
|
||||
# Use JSON.parse to get a the json object.
|
||||
def ClassyFireAPI.get_sequence_classification(fingerprint,format="json")
|
||||
begin
|
||||
if format == "json"
|
||||
|
|
@ -102,6 +98,11 @@ module ClassyFireAPI
|
|||
end
|
||||
end
|
||||
|
||||
# Retrieves the classification results for a given chemical entity.
|
||||
#
|
||||
# @param the InChIKey [String] of the entity
|
||||
# @param The format [String] the format of the query (Only JSON)
|
||||
# @return [Text] A text file displaying the classification results for the entity in the specified format.
|
||||
def ClassyFireAPI.get_entity_classification(inchikey,format="json")
|
||||
inchikey_id = inchikey.to_s.gsub('InChIKey=','')
|
||||
begin
|
||||
|
|
@ -156,36 +157,43 @@ module ClassyFireAPI
|
|||
input = []
|
||||
|
||||
lines = File.readlines(absolute_path)
|
||||
|
||||
i = 0
|
||||
lines.uniq.each do |line|
|
||||
i += 1
|
||||
sline = line.strip.split("\t")
|
||||
if sline.length == 1
|
||||
input <<"#{sline[0]}"
|
||||
elsif sline.length >= 2
|
||||
input <<"#{sline[1]}\t#{sline[0]}"
|
||||
elsif sline.length == 2
|
||||
#ID\tSMILES (OR INCHI, OR VALID IUPAC NAME)
|
||||
input <<"#{sline[0]}\t#{sline[1]}"
|
||||
end
|
||||
input <<"#{sline[0]}"
|
||||
end
|
||||
|
||||
query_ids = []
|
||||
subdivised_groups = input.uniq.each_slice(slice_length).to_a
|
||||
puts "nr of subdivised_groups: #{subdivised_groups.length}"
|
||||
puts subdivised_groups[0]
|
||||
sleeping_time = 360
|
||||
initial_nr_of_jobs = 40
|
||||
# puts subdivised_groups[0]
|
||||
sleeping_time = 240
|
||||
initial_nr_of_jobs = 30
|
||||
i = start
|
||||
|
||||
while i < initial_nr_of_jobs
|
||||
|
||||
title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"
|
||||
|
||||
if i <= subdivised_groups.length
|
||||
begin
|
||||
puts "\n\n\n\n---------------------- -----------"
|
||||
# begin
|
||||
puts "submitting #{title}"
|
||||
puts subdivised_groups[i-1].join("\n")
|
||||
q = submit_query(title,subdivised_groups[i-1].join("\n"),type)
|
||||
# puts q
|
||||
query_ids << JSON.parse(q)['id']
|
||||
rescue Exception => e
|
||||
puts e.message
|
||||
puts e.backtrace.inspect
|
||||
end
|
||||
# rescue Exception => e
|
||||
# puts e.message
|
||||
# puts e.backtrace.inspect
|
||||
# end
|
||||
i = i + 1
|
||||
else
|
||||
break
|
||||
|
|
@ -198,7 +206,7 @@ module ClassyFireAPI
|
|||
|
||||
while i >= initial_nr_of_jobs && i < subdivised_groups.length
|
||||
k = 0
|
||||
for k in (i..(i+80))
|
||||
for k in (i..(i + initial_nr_of_jobs))
|
||||
title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{k}"
|
||||
i = i + 1
|
||||
begin
|
||||
|
|
@ -241,71 +249,6 @@ module ClassyFireAPI
|
|||
end
|
||||
|
||||
|
||||
# Takes a tab-separated file and submit randomly selected structures in bulks of a given size.
|
||||
#
|
||||
# For 'STRUCTURE' or 'IUPAC_NAME'query types, each line must contain either
|
||||
# 1) Only a structural represenation: SMILES, InChI for the 'STRUCTURE' query_type or a IUPAC name
|
||||
# for the 'IUPAC NAME' query type.
|
||||
# 2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
|
||||
# 'STRUCTURE' query_type or a IUPAC name for the 'IUPAC NAME' query type.
|
||||
#
|
||||
# For 'FASTA' query type, just submit the query as a standard FASTA text.
|
||||
# @param tab_separated_input_file [Text] The path to the input file.
|
||||
# @param size [Integer] The maximum number of entries for each query input (the whole file
|
||||
# is fragmented into n part of #slice_length entries each).
|
||||
# @param type [String] The query_type, 'STRUCTURE' (default) or 'IUPAC_NAME' or 'FASTA'.
|
||||
def ClassyFireAPI.submit_random_subset_of_query_input_in_chunks(tab_separated_input_file,size, type='STRUCTURE')
|
||||
@start_time = Time.now
|
||||
absolute_path = File.expand_path(tab_separated_input_file)
|
||||
f = File.open(absolute_path, 'r')
|
||||
input = []
|
||||
|
||||
f.each_line do |line|
|
||||
|
||||
sline = line.strip.split("\t")
|
||||
if sline.length == 1
|
||||
input <<"#{sline[0]}"
|
||||
elsif sline.length == 2
|
||||
input <<"#{sline[0]}\t#{sline[1]}"
|
||||
end
|
||||
end
|
||||
|
||||
query_ids = []
|
||||
indexes = []
|
||||
r = 1
|
||||
while r <= (size)
|
||||
s = rand(0..(input.length - 1))
|
||||
unless indexes.include?(s)
|
||||
indexes<<s
|
||||
r += 1
|
||||
end
|
||||
end
|
||||
|
||||
random_subset = indexes.map{|x| input[x]}
|
||||
subdivised_groups = random_subset.each_slice(100).to_a
|
||||
sleeping_time = 120
|
||||
|
||||
i = 0
|
||||
while i < subdivised_groups.length
|
||||
k = 0
|
||||
for k in (i..(i + 5))
|
||||
title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{k+1}"
|
||||
i = i + 1
|
||||
begin
|
||||
puts "submitting #{title}"
|
||||
q = submit_query(title,subdivised_groups[k].join("\n"),type)
|
||||
rescue Exception => e
|
||||
puts e.message
|
||||
puts e.backtrace.inspect
|
||||
end
|
||||
end
|
||||
i = k
|
||||
puts "Going to sleep at #{Time.now - @start_time} for #{sleeping_time} s."
|
||||
sleep(sleeping_time)
|
||||
puts "Waking up at #{Time.now - @start_time}"
|
||||
end
|
||||
end
|
||||
|
||||
# Reads a tab separated file, and use the structure representation
|
||||
#to retrieve the strutcure's classification from ClassyFire.
|
||||
#
|
||||
|
|
@ -405,7 +348,6 @@ module ClassyFireAPI
|
|||
# puts "#{key} :: #{h[key]}"
|
||||
begin
|
||||
inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
|
||||
# inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
|
||||
# puts inchikey
|
||||
qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json"))
|
||||
qr['identifier'] = key
|
||||
|
|
@ -421,7 +363,6 @@ module ClassyFireAPI
|
|||
# puts "#{key} :: #{h[key]}"
|
||||
begin
|
||||
inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
|
||||
# inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
|
||||
# puts inchikey
|
||||
qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json"))
|
||||
qr['identifier'] = key
|
||||
|
|
@ -464,7 +405,6 @@ module ClassyFireAPI
|
|||
# puts "#{key} :: #{h[key]}"
|
||||
begin
|
||||
inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
|
||||
# inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
|
||||
# puts inchikey
|
||||
qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf")
|
||||
if qr.include?("The page you were looking for doesn't exist")
|
||||
|
|
@ -485,7 +425,6 @@ module ClassyFireAPI
|
|||
key = h.keys[-1]
|
||||
begin
|
||||
inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
|
||||
# inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
|
||||
# puts inchikey
|
||||
qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf")
|
||||
if qr.include?("The page you were looking for doesn't exist")
|
||||
|
|
@ -504,3 +443,7 @@ module ClassyFireAPI
|
|||
end
|
||||
end
|
||||
end
|
||||
|
||||
if __FILE__ == $0
|
||||
|
||||
end
|
||||
|
|
|
|||
|
|
@ -0,0 +1,8 @@
|
|||
require 'active_resource'
|
||||
require 'rest-client'
|
||||
|
||||
class NodeResource < ActiveResource::Base
|
||||
self.site ='http://classyfire.wishartlab.com'
|
||||
self.element_name = "tax_node"
|
||||
has_many :entities, class_name: 'EntityResource'
|
||||
end
|
||||
Loading…
Reference in New Issue