biointerchange 0.2.1 → 0.2.2

data/web/ontologies.html

@@ -31,34 +31,14 @@
     <div class="navbar navbar-inverse navbar-fixed-top">
       <div class="navbar-inner">
         <div class="container">
-          <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </a>
           <a class="brand" href="index.html">BioInterchange</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li><a href="index.html">Home</a></li>
-              <li class="active"><a href="ontologies.html">Ontologies</a></li>
-              <li><a href="about.html">About</a></li>
-              <!--
-              <li class="dropdown">
-                <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
-                <ul class="dropdown-menu">
-                  <li><a href="#">To</a></li>
-                  <li><a href="#">Be</a></li>
-                  <li><a href="#">Done</a></li>
-                  <li><a href="#">Dude</a></li>
-                  <li class="divider"></li>
-                  <li class="nav-header">API</li>
-                  <li><a href="#">API usage information</a></li>
-                  <li><a href="#">Implementing new readers/writers</a></li>
-                </ul>
-              </li>
-              -->
-            </ul>
-          </div><!--/.nav-collapse -->
+          <ul class="nav">
+            <li><a href="cli.html">Shell Tool</a></li>
+            <li><a href="webservices.html">Web-Services</a></li>
+            <li><a href="api.html">API</a></li>
+            <li class="active"><a href="ontologies.html">Ontologies</a></li>
+            <li><a href="about.html">About</a></li>
+          </ul>
         </div>
       </div>
     </div>
@@ -69,7 +49,7 @@
       <div class="row">
         <div class="span12">
           <h2>Ontologies</h2>
-          <p>BioInterchange makes use of external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project, and ontologies that we designed and implemented for specific file format conversion purposes. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and contributions of ontologies that permit including more file formats for RDF conversion are most welcome.</p>
+          <p>BioInterchange makes use of external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project, as well as ontologies that we designed and implemented for specific file format conversion purposes. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and contributions of ontologies that permit including more file formats for RDF conversion are most welcome.</p>
           <h3>BioInterchange Ontologies</h3>
           Some ontologies have been specifically designed and implemented for BioInterchange and are freely available via the <a href="http://creativecommons.org/licenses/by-sa/3.0/">Creative Commons Attribution Share-Alike</a> (<a href="http://creativecommons.org/licenses/by-sa/3.0/">CC BY-SA</a>) license. The listing below gives an overview of the ontologies we created, where more information about them is available on their <a href="http://biointerchange.github.com/Ontologies">GitHub project pages</a>.
           <h4>Generic Feature Format Version 3 Ontology</h4>
@@ -93,7 +73,7 @@
       <hr>
 
       <footer>
-        <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
       </footer>
 
     </div> <!-- /container -->

data/web/service/rdfizer.fcgi

@@ -6,12 +6,21 @@ require 'uri'
 require 'cgi'
 require 'fcgi'
 
+# So, these requires are also in the GFF3 writer. Figure out why "load"
+# appears to ignore those and I have to explicitly re-state them here.
+require 'rdf'
+require 'rdf/ntriples'
+
 # This will be obsolete once BioInterchange has been turned into a gem:
 load '../../lib/biointerchange/core.rb'
-load '../../lib/biointerchange/gff3.rb'
+load '../../lib/biointerchange/faldo.rb'
+load '../../lib/biointerchange/gff3o.rb'
+load '../../lib/biointerchange/gvf1o.rb'
 load '../../lib/biointerchange/sio.rb'
+load '../../lib/biointerchange/so.rb'
 load '../../lib/biointerchange/sofa.rb'
 load '../../lib/biointerchange/reader.rb'
+load '../../lib/biointerchange/model.rb'
 load '../../lib/biointerchange/writer.rb'
 load '../../lib/biointerchange/textmining/text_mining_reader.rb'
 load '../../lib/biointerchange/textmining/pubannos_json_reader.rb'
@@ -22,17 +31,24 @@ load '../../lib/biointerchange/textmining/document.rb'
 load '../../lib/biointerchange/textmining/process.rb'
 load '../../lib/biointerchange/genomics/gff3_feature.rb'
 load '../../lib/biointerchange/genomics/gff3_feature_set.rb'
+load '../../lib/biointerchange/genomics/gff3_pragmas.rb'
 load '../../lib/biointerchange/genomics/gff3_reader.rb'
+load '../../lib/biointerchange/genomics/gvf_feature.rb'
+load '../../lib/biointerchange/genomics/gvf_feature_set.rb'
+load '../../lib/biointerchange/genomics/gvf_pragmas.rb'
+load '../../lib/biointerchange/genomics/gvf_reader.rb'
 load '../../lib/biointerchange/genomics/gff3_rdf_ntriples.rb'
 
 input_formats = {}
 input_formats['dbcls.catanns.json'] = [ BioInterchange::TextMining::PubannosJsonReader, 'name', 'name_id', 'date', [ Proc.new { |*args| BioInterchange::TextMining::TMReader::determine_process(*args) }, 'name_id' ], 'version' ]
 input_formats['uk.ac.man.pdfx'] = [ BioInterchange::TextMining::PdfxXmlReader, 'name', 'name_id', 'date', [ Proc.new { |*args| BioInterchange::TextMining::TMReader::determine_process(*args) }, 'name_id' ], 'version' ]
 input_formats['biointerchange.gff3'] = [ BioInterchange::Genomics::GFF3Reader, 'name', 'name_uri', 'date' ]
+input_formats['biointerchange.gvf'] = [ BioInterchange::Genomics::GVFReader, 'name', 'name_uri', 'date' ]
 
 output_formats = {}
 output_formats['rdf.bh12.sio'] = BioInterchange::TextMining::RDFWriter
 output_formats['rdf.biointerchange.gff3'] = BioInterchange::Genomics::RDFWriter
+output_formats['rdf.biointerchange.gvf'] = BioInterchange::Genomics::RDFWriter
 
 FCGI.each { |fcgi|
   request = fcgi.in.read
@@ -42,7 +58,8 @@ FCGI.each { |fcgi|
 
   begin
     request = JSON.parse(request)
-    parameters = JSON.parse(URI.decode(request['parameters']))
+    parameters = request['parameters']
+    parameters = JSON.parse(URI.decode(parameters)) if parameters.kind_of?(String)
     data = URI.decode(request['data'])
 
     raise ArgumentError, 'An input format must be given in the meta-data using the key "input".' unless parameters['input']

data/web/webservices.html

@@ -32,34 +32,14 @@
     <div class="navbar navbar-inverse navbar-fixed-top">
       <div class="navbar-inner">
         <div class="container">
-          <a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </a>
           <a class="brand" href="index.html">BioInterchange</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li class="active"><a href="index.html">Home</a></li>
-              <li><a href="ontologies.html">Ontologies</a></li>
-              <li><a href="about.html">About</a></li>
-              <!--
-              <li class="dropdown">
-                <a href="#" class="dropdown-toggle" data-toggle="dropdown">Documentation <b class="caret"></b></a>
-                <ul class="dropdown-menu">
-                  <li><a href="#">To</a></li>
-                  <li><a href="#">Be</a></li>
-                  <li><a href="#">Done</a></li>
-                  <li><a href="#">Dude</a></li>
-                  <li class="divider"></li>
-                  <li class="nav-header">API</li>
-                  <li><a href="#">API usage information</a></li>
-                  <li><a href="#">Implementing new readers/writers</a></li>
-                </ul>
-              </li>
-              -->
-            </ul>
-          </div><!--/.nav-collapse -->
+          <ul class="nav">
+            <li><a href="cli.html">Shell Tool</a></li>
+            <li class="active"><a href="webservices.html">Web-Services</a></li>
+            <li><a href="api.html">API</a></li>
+            <li><a href="ontologies.html">Ontologies</a></li>
+            <li><a href="about.html">About</a></li>
+          </ul>
         </div>
       </div>
     </div>
@@ -72,22 +52,26 @@
           <h1>Web-Services</h1>
           <p>Two query points to access BioInterchange are provided on the internet:
             <ol>
-              <li>an interactive web-interface</li>
-              <li>a RESTful web-service</li>
+              <li><a href="#interface">an interactive web-interface</a></li>
+              <li><a href="#webservice">a RESTful web-service</a></li>
             </ol>
           </p>
-          <h3>Interactive Web-Interface</h3>
+          <p>The interactive web-interfaces makes use of the RESTful web-service.
+          </p>
+          <h3 id="interface">Interactive Web-Interface</h3>
           <p>Select the input format of the data:<br />
             <select id="inputformat" style="min-width: 50%;" onchange="selectDbclsCatannsJson();">
               <option value="dbcls.catanns.json" selected>DBCLS PubAnnotation's Category Annotations (catanns) JSON</option>
               <option value="biointerchange.gff3">GFF3</option>
+              <option value="biointerchange.gvf">GVF</option>
               <option value="uk.ac.man.pdfx">PDFx XML</option>
             </select><br />
             Select the RDF serialization method (output format):<br />
             <span class="muted">Not all output format are supported for a given input format. Invalid choices are disabled automatically here.</span><br />
             <select id="outputformat" style="min-width: 50%;">
               <option id="output.rdf.bh12.sio" value="rdf.bh12.sio" selected>RDF using SIO and FOAF ontologies</option>
-              <option id="output.rdf.biointerchange.gff3" value="rdf.biointerchange.gff3" disabled>RDF using GFF3 ontology</option>
+              <option id="output.rdf.biointerchange.gff3" value="rdf.biointerchange.gff3" disabled>RDF using GFF3O ontology</option>
+              <option id="output.rdf.biointerchange.gvf" value="rdf.biointerchange.gvf" disabled>RDF using GVF1O ontology</option>
             </select><br />
             <a class="btn btn-info" onclick="pasteExample();">Paste Input-Specific Example</a>
           </p>
@@ -99,18 +83,69 @@
             <br /><br />
             RDF output:<br />
             <a class="btn btn-primary" onclick="generateRDF();">Generate RDF</a>
-            <pre id="output" style="font-size: 75%; width: 100%; min-height: 50px;"><i>RDF output will be <b>concatenated</b> here...</i></pre>
             <a class="btn" onclick="$('#output').empty();">Clear RDF</a>
+            <pre id="output" style="font-size: 75%; width: 100%; min-height: 50px;"><i>RDF output will be <b>concatenated</b> here...</i></pre>
+          </p>
+          <h3 id="webservice">RESTful Web-Service</h3>
+          <p>
+            A RESTful web-service is available via the URI: <code>http://www.biointerchange.org/service/rdfizer.biocgi</code>
+          </p>
+          <p>
+            RDFization parameters and data are send as a single HTTP POST requests containing a JSON object. The JSON object has to be formatted as follows:
+<pre>
+{
+  "parameters" : {
+    "input" : "INPUT_FORMAT",
+    "output": "OUTPUT_METHOD"
+  },
+  "data" : "URL_ENCODED_DATA"
+}
+</pre>
+            <ul>
+              <li><code>INPUT_FORMAT</code>: determines the input data type; available input formats are</li>
+              <ul>
+                <li><code>biointerchange.gff3</code>: <a href="http://www.sequenceontology.org/resources/gff3.html">Generic Feature Format Version 3</a></li>
+                <li><code>biointerchange.gvf</code>: <a href="http://www.sequenceontology.org/resources/gvf.html">Genome Variation Format</a></li>
+                <li><code>dbcls.catanns.json</code>: <a href="http://pubannotation.dbcls.jp">PubAnnotation categorical annotations</a></li>
+                <li><code>uk.ac.man.pdfx</code>: <a href=http://pdfx.cs.man.ac.uk">PDFx</a></li>
+              </ul>
+              <li><code>OUTPUT_METHOD</code>: determines the RDFization method that should be used, output will always be RDF N-Triples; available output formats are</li>
+              <ul>
+                <li><code>rdf.biointerchange.gff3</code>: RDFization of <code>biointerchange.gff3</code></li>
+                <li><code>rdf.biointerchange.gvf</code>: RDFization of <code>biointerchange.gvf</code></li>
+                <li><code>rdf.bh12.sio</code>: RDFization of <code>dbcls.catanns.json</code> or <code>uk.ac.man.pdfx</code></li>
+              </ul>
+              <li><code>URL_ENCODED_DATA</code>: data for RDFization as <a href="http://en.wikipedia.org/wiki/Percent-encoding">URL encoded</a> string</li>
+            </ul>
+          </p>
+          <h4>Example</h4>
+          <p>
+              A query example is part of BioInterchange's source repository. The file [webservice_example.json](https://raw.github.com/BioInterchange/BioInterchange/master/examples/webservice_example.json) contains the following query:
+
+<pre>
+{
+    "parameters" : {
+      "input" : "biointerchange.gff3",
+      "output": "rdf.biointerchange.gff3"
+    },
+    "data" : "ChrX.38%09bovine_complete_cds_gmap_perfect%09gene%0915870%0916254%09.%09+%09.%09ID%3DBC109609_ChrX.38%0AChrX.38%09bovine_complete_cds_gmap_perfect%09mRNA%0915870%0916254%09.%09+%09.%09ID%3Dbovine_complete_cds_gmap_perfect_BC109609_ChrX.38%3BParent%3DBC109609_ChrX.38%0AChrX.38%09bovine_complete_cds_gmap_perfect%09CDS%0915870%0916254%09.%09+%090%09Parent%3Dbovine_complete_cds_gmap_perfect_BC109609_ChrX.38%0AChrX.38%09bovine_complete_cds_gmap_perfect%09exon%0915870%0916254%09.%09+%090%09Parent%3Dbovine_complete_cds_gmap_perfect_BC109609_ChrX.38%0A"
+}
+</pre>
+          </p>
+          <p>
+            The query can be run using the popular [cURL](http://en.wikipedia.org/wiki/CURL) tool:
+
+<pre>
+curl -d '@webservice_example.json' http://www.biointerchange.org/service/rdfizer.biocgi
+</pre>
           </p>
-          <h3>RESTful Web-Service</h3>
-          <p>TODO</p>
         </div>
       </div>
 
       <hr>
 
       <footer>
-        <p>&copy; <a href="https://github.com/BioInterchange/BioInterchange#contributors">The BioInterchange Contributors</a> 2012</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
       </footer>
 
     </div> <!-- /container -->

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biointerchange
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.2
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-20 00:00:00.000000000 Z
+date: 2013-05-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rdf
@@ -179,6 +179,7 @@ files:
 - VERSION
 - bin/biointerchange
 - examples/BovineGenomeChrX.gff3.gz
+- examples/Saccharomyces_cerevisiae_incl_consequences.gvf.gz
 - examples/chromosome_BF.gff
 - examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
 - examples/gb-2007-8-3-R40.xml
@@ -186,13 +187,16 @@ files:
 - examples/pubannotation.10096561.json.old
 - examples/pubannotation.2626671.json
 - examples/vocabulary.rb
+- examples/webservice_example.json
 - generators/GOxrefify.rb
 - generators/javaify.rb
+- generators/make_supplement_releases.rb
 - generators/pythonify.rb
 - generators/rdfxml.rb
 - lib/biointerchange.rb
 - lib/biointerchange/core.rb
 - lib/biointerchange/exceptions.rb
+- lib/biointerchange/faldo.rb
 - lib/biointerchange/genomics/gff3_feature.rb
 - lib/biointerchange/genomics/gff3_feature_set.rb
 - lib/biointerchange/genomics/gff3_pragmas.rb
@@ -205,6 +209,7 @@ files:
 - lib/biointerchange/gff3o.rb
 - lib/biointerchange/goxref.rb
 - lib/biointerchange/gvf1o.rb
+- lib/biointerchange/model.rb
 - lib/biointerchange/reader.rb
 - lib/biointerchange/registry.rb
 - lib/biointerchange/sio.rb
@@ -228,14 +233,18 @@ files:
 - supplemental/java/biointerchange/pom.xml
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/App.java
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/AppSIO.java
+- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
+- supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java
 - supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java
 - supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java
 - supplemental/python/biointerchange/__init__.py
+- supplemental/python/biointerchange/faldo.py
 - supplemental/python/biointerchange/gff3o.py
+- supplemental/python/biointerchange/goxref.py
 - supplemental/python/biointerchange/gvf1o.py
 - supplemental/python/biointerchange/sio.py
 - supplemental/python/biointerchange/so.py
@@ -254,6 +263,7 @@ files:
 - web/bootstrap/js/bootstrap.js
 - web/bootstrap/js/bootstrap.min.js
 - web/bootstrap/js/jquery-1.8.1.min.js
+- web/cli.html
 - web/css/rdoc-style.css
 - web/css/rdoc.css
 - web/images/BioInterchange300.png
@@ -276,7 +286,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3573974347374072968
+      hash: -3312965476220723123
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: