biointerchange 0.2.1 → 0.2.2

data/README.md

@@ -7,6 +7,8 @@ BioInterchange is a tool for generating interchangable RDF data from non-RDF dat
 
 Supported input file formats (see examples directory):
 
+* [GFF3](http://www.sequenceontology.org/resources/gff3.html)
+* [GVF](http://www.sequenceontology.org/resources/gvf.html)
 * [Pubannos JSON](http://pubannotation.dbcls.jp/)
 * [PDFx XML](http://pdfx.cs.man.ac.uk/)
 
@@ -19,6 +21,7 @@ Ontologies used in the RDF output:
 * [Generic Feature Format Version 3 Ontology](http://www.biointerchange.org/ontologies.html) (GFF3O)
 * [Genome Variation Format Version 1 Ontology](http://www.biointerchange.org/ontologies.html) (GVF1O)
 * [Semanticscience Integrated Ontology](http://code.google.com/p/semanticscience/wiki/SIO) (SIO)
+* [Sequence Ontology](http://www.sequenceontology.org/index.html) (SO)
 * [Sequence Ontology Feature Annotation](http://www.sequenceontology.org/index.html) (SOFA)
 
 #### Contributing
@@ -96,7 +99,8 @@ The following list provides information on the origin of the example-data files
 *  `BovineGenomeChrX.gff3.gz`: Gzipped GFF3 file describing a Bos taurus chromosome X. Downloaded from [http://bovinegenome.org/?q=download_chromosome_gff3](http://bovinegenome.org/?q=download_chromosome_gff3)
 *  `chromosome_BF.gff`: GFF3 file of floating contigs from the Baylor Sequencing Centre. Downloaded from [http://dictybase.org/Downloads](http://dictybase.org/Downloads)
 *  `estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf`: GVF file of EBI's [DGVa](http://www.ebi.ac.uk/dgva/database-genomic-variants-archive). Downloaded from [ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd176_Banerjee_et_al_2011/gvf/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf](ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd176_Banerjee_et_al_2011/gvf/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf)
-*  `gb-2007-8-3-R40.xml`: Generated by [pdfx](http://pdfx.cs.man.ac.uk) from open-access source PDF [Sense-antisense pairs in mammals: functional and evolutionary considerations](http://genomebiology.com/content/pdf/gb-2007-8-3-r40.pdf)
+*  `gb-2007-8-3-R40.xml`: Generated by [PDFx](http://pdfx.cs.man.ac.uk) from open-access source PDF [Sense-antisense pairs in mammals: functional and evolutionary considerations](http://genomebiology.com/content/pdf/gb-2007-8-3-r40.pdf)
+*  `Saccharomyces_cerevisiae_incl_consequences.gvf.gz`: Downloaded from [ftp://ftp.ensembl.org/pub/release-71/variation/gvf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae_incl_consequences.gvf.gz](ftp://ftp.ensembl.org/pub/release-71/variation/gvf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae_incl_consequences.gvf.gz)
 
 ### Application Programming Interface
 
@@ -118,7 +122,7 @@ BioInterchange available.
 To install the BioInterchange egg, run:
 
     sudo easy_install rdflib
-    sudo easy_install http://www.biointerchange.org/eggs/biointerchange-0.1.2-py2.7.egg
+    sudo easy_install http://www.biointerchange.org/eggs/biointerchange-0.2.2-py2.7.egg
 
 Usage examples:
 
@@ -159,7 +163,7 @@ To use the BioInterchange artifact, set-up add the following to your Maven POM f
       <dependency>
         <groupId>org.biointerchange</groupId>
         <artifactId>vocabularies</artifactId>
-        <version>0.1.2</version>
+        <version>0.2.2</version>
       </dependency>
     </dependencies>
 
@@ -231,11 +235,55 @@ Usage examples of accessing GFF3O's vocabulary:
 
 ### RESTful Web-Service
 
-TODO
+A RESTful web-service is available via the URI: [http://www.biointerchange.org/service/rdfizer.biocgi](http://www.biointerchange.org/service/rdfizer.biocgi)
+
+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:
+
+    {
+      "parameters" : {
+        "input" : "INPUT_FORMAT",
+        "output": "OUTPUT_METHOD"
+      },
+      "data" : "URL_ENCODED_DATA"
+    }
+
+*  `INPUT_FORMAT`: determines the input data type; available input formats are
+   *  `biointerchange.gff3`: [Generic Feature Format Version 3](http://www.sequenceontology.org/resources/gff3.html)
+   *  `biointerchange.gvf`: [Genome Variation Format](http://www.sequenceontology.org/resources/gvf.html)
+   *  `dbcls.catanns.json`: [PubAnnotation categorical annotations](http://pubannotation.dbcls.jp) JSON
+   *  `uk.ac.man.pdfx`: [PDFx](http://pdfx.cs.man.ac.uk) XML
+*  `OUTPUT_METHOD`: determines the RDFization method that should be used, output will always be RDF N-Triples; available output formats are
+   *  `rdf.biointerchange.gff3`: RDFization of `biointerchange.gff3`
+   *  `rdf.biointerchange.gvf`: RDFization of `biointerchange.gvf`
+   *  `rdf.bh12.sio`: RDFization of `dbcls.catanns.json` or `uk.ac.man.pdfx`
+*  `URL_ENCODED_DATA`: data for RDFization as [URL encoded](http://en.wikipedia.org/wiki/Percent-encoding) string
+
+#### Example
+
+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:
+
+    {
+        "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"
+    }
+
+The query can be run using the popular [cURL](http://en.wikipedia.org/wiki/CURL) tool:
+
+    curl -d '@webservice_example.json' http://www.biointerchange.org/service/rdfizer.biocgi
 
 ### Interactive Web-Site
 
-TODO
+BioInterchange has an [interactive web-interface](http://www.biointerchange.org/webservices.html) for RDFizing small amounts of data. Each input format and RDF serialization method pair comes with an example, which can be used as a guidance or test bed for learning how to use BioInterchange.
+
+#### Usage Instructions
+
+1.  select a data input format (for example, GFF3)
+2.  select a RDF serialization method/output format (for example, "RDF using GFF3O ontology")
+3.  paste RDF serialization method parameters and data in the text fields (or, click "Paste Input-Specific Example")
+4.  click "Generate RDF" and the RDFized data will appear below
 
 Build Notes
 -----------
@@ -262,10 +310,15 @@ The last step, `bundle`, will install gem dependencies of BioInterchange automat
 
 ### Building Vocabulary Classes
 
-Building a new version of the Ruby vocabulary classes for GFF3, SIO, SOFA (requires that the OBO files are saves as RDF/XML using [Protege](http://protege.stanford.edu)):
+Building a new version of the Ruby vocabulary classes for FALDO, GFF3O, GVF1O, SIO, SOFA (requires that the OBO files are saves as RDF/XML using [Protege](http://protege.stanford.edu); Apache [Jena](http://jena.apache.org)'s `rdfcat` tool is required to reformat RDF Turtle as RDF/XML):
 
     sudo gem install rdf
     sudo gem install rdf-rdfxml
+    echo -e "require 'rdf'\nmodule BioInterchange\n" > lib/biointerchange/faldo.rb
+    rdfcat -ttl <path-to-turtle-version-of-faldo> > faldo.xml.tmp
+    ruby generators/rdfxml.rb faldo.xml.tmp FALDO >> lib/biointerchange/faldo.rb
+    rm -f faldo.xml.tmp
+    echo -e "\nend" >> lib/biointerchange/faldo.rb
     echo -e "require 'rdf'\nmodule BioInterchange\n" > lib/biointerchange/gff3o.rb
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O >> lib/biointerchange/gff3o.rb
     echo -e "\nend" >> lib/biointerchange/gff3o.rb
@@ -292,12 +345,7 @@ A Geno Ontology external reference (GOxref) vocabulary can be created by directl
 
 The source-code generation can be skipped, if none of the ontologies that are used by BioInterchange have been changed. Otherwise, the existing Python vocabulary class wrappers can be generated as follows:
 
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gff3o.py
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gvf1o.py
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/pythonify.rb > supplemental/python/biointerchange/sio.py
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/pythonify.rb > supplemental/python/biointerchange/so.py
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/pythonify.rb > supplemental/python/biointerchange/sofa.py
-    curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/pythonify.rb > supplemental/python/biointerchange/goxref.py
+    ruby generators/make_supplement_releases.rb
 
 Generate the BioInterchange Python vocabulary egg:
 
@@ -314,12 +362,7 @@ The vocabulary wrapper makes used of RDFLib, which does not install automaticall
 
 The source-code generation can be skipped, if none of the ontologies that are used by BioInterchange have been changed. Otherwise, the existing Java vocabulary class wrappers can be generated as follows:
 
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/javaify.rb "http://purl.obolibrary.org/obo/" > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java
-    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/javaify.rb "http://purl.obolibrary.org/obo/" > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java
-    curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java
+    ruby generators/make_supplement_releases.rb
 
 Generate the BioInterchange Java vocabulary artifact:
 

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/examples/webservice_example.json

@@ -0,0 +1,7 @@
+{
+  "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"
+}

data/generators/GOxrefify.rb

@@ -1,41 +1,49 @@
 #!/usr/bin/ruby
 
 def record(id, description, uri)
-  puts "  # Returns the link-out URI for objects of \"#{description}\"."
-  puts "  def self.#{id}"
-  puts "    RDF::URI.new(\"#{uri}\")"
-  puts '  end'
-  puts ''
+  cls = "  # Returns the link-out URI for objects of \"#{description}\".\n"
+  cls << "  def self.#{id}\n"
+  cls << "    RDF::URI.new(\"#{uri}\")\n"
+  cls << "  end\n\n"
+
+  cls
 end
 
-puts 'class GOXRef'
-puts ''
+def goxrefify(ontology)
+  cls = "class GOXRef\n\n"
+
+  in_record = false
 
-in_record = false
+  id = nil
+  description = nil
+  uri = nil
 
-id = nil
-description = nil
-uri = nil
+  ontology.each { |line|
+    line.chomp!
 
-STDIN.each { |line|
-  line.chomp!
+    if line.empty? then
+      record(id, description, uri) if uri and not uri.match(/\[.*\]/)
+      uri = nil
+      in_record = false
+    end
 
-  if line.empty? then
-    record(id, description, uri) if uri and not uri.match(/\[.*\]/)
-    uri = nil
-    in_record = false
-  end
+    if line.start_with?('abbreviation:') and not in_record then
+      id = line.sub(/^abbreviation: /, '').gsub(/[-\/]/, '_')
+      in_record = true
+    end
+    
+    description = line.sub(/^database: /, '') if line.start_with?('database:') and in_record
+    uri = line.sub(/^url_syntax: /, '').sub(/\[example_id\]$/, '') if line.start_with?('url_syntax:') and in_record
+  }
 
-  if line.start_with?('abbreviation:') and not in_record then
-    id = line.sub(/^abbreviation: /, '').gsub(/[-\/]/, '_')
-    in_record = true
-  end
-  
-  description = line.sub(/^database: /, '') if line.start_with?('database:') and in_record
-  uri = line.sub(/^url_syntax: /, '').sub(/\[example_id\]$/, '') if line.start_with?('url_syntax:') and in_record
-}
+  cls << record(id, description, uri) if uri
 
-record(id, description, uri) if uri
+  cls << "end\n"
 
-puts 'end'
+  cls
+end
+
+unless @loaded_externally then
+  puts goxrefify(STDIN)
+end
 

data/generators/javaify.rb

@@ -1,131 +1,150 @@
 #!/usr/bin/ruby
 
-private_scope = false
-java_class = nil
-namespace = nil
-comment = nil
+def javaify(rubycode, namespace = nil)
+  private_scope = false
+  java_class = nil
+  comment = nil
 
-if ARGV.length == 1 then
-  namespace = ARGV[0]
-end
+  namespace_wrapper_generated = false
+  class_closed = false
 
-cls = ''
+  cls = <<EOS
+package org.biointerchange.vocabulary;
+import java.util.Arrays;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections.Predicate;
 
-puts 'package org.biointerchange.vocabulary;'
-puts ''
-puts 'import java.util.Arrays;'
-puts 'import java.util.Map;'
-puts 'import java.util.HashMap;'
-puts 'import java.util.HashSet;'
-puts 'import java.util.Set;'
-puts 'import com.hp.hpl.jena.rdf.model.Property;'
-puts 'import com.hp.hpl.jena.rdf.model.Resource;'
-puts 'import com.hp.hpl.jena.rdf.model.ResourceFactory;'
-puts 'import org.apache.commons.collections.CollectionUtils;'
-puts 'import org.apache.commons.collections.Predicate;'
-puts ''
+EOS
 
-STDIN.each { |line|
-  line.chomp!
+  rubycode.each { |line|
+    line.chomp!
 
-  if line.match('http://') then
-    if line.match(/http:\/\/[^'")]+#[^'")]+/) then
-      namespace = line.scan(/http:\/\/[^'")]+/)[0].sub(/(#).*$/, '\1') unless namespace
-    else
-      namespace = line.scan(/http:\/\/[^'")]+/)[0].sub(/\/[^\/]+$/, '/') unless namespace
-    end
-    if line.match("#{namespace}\w+") then
-      line.gsub!(namespace, '') unless line.strip.start_with?('#')
-    end
-  end
+    next if line.start_with?('module ') or line.start_with?('require ')
 
-  if line.start_with?('class') then
-    java_class = line.sub(/^.* /, '')
-    transduction = "public class #{java_class} {"
-  elsif line.strip.start_with?('def ') then
-    leading_spaces = line.gsub(/[^ ].*$/, '')
-    transduction = ''
-    if comment then
-      transduction << "#{("/**\n *" + comment).gsub(/^/, "#{leading_spaces}")}\n#{leading_spaces} */\n"
-      comment = nil
-    end
-    transduction << "  public static #{line.sub('?', '').sub(/self\./, '').sub(/ *def\ /, '')}"
-    method_name = transduction.sub(/^.*public static /m, '').sub(/(\(.*)?$/, '')
-    transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode|byte|char|short|int|long|float|double|boolean)$/)
-    variables = transduction.scan(/^\s*public static \w+\((.+)\)$/)
-    variables = variables[0][0].split(',').map { |variable| variable.strip } if variables.length > 0
-    if method_name == 'is_object_property' then
-      transduction.sub!(/public static .*$/, "public static boolean isObjectProperty(Resource #{variables[0]})")
-    elsif method_name == 'is_datatype_property' then
-      transduction.sub!(/public static .*$/, "public static boolean isDatatypeProperty(Resource #{variables[0]})")
-    elsif method_name == 'is_class' then
-      transduction.sub!(/public static .*$/, "public static boolean isClass(Resource #{variables[0]})")
-    elsif method_name == 'is_named_individual' then
-      transduction.sub!(/public static .*$/, "public static boolean isNamedIndividual(Resource #{variables[0]})")
-    elsif method_name == 'with_parent' then
-      transduction.sub!(/public static .*$/, "public static Set<Resource> withParent(Set<Resource> #{variables[0]}, final Resource #{variables[1]})")
-    elsif method_name == 'has_parent' then
-      transduction.sub!(/public static .*$/, "public static boolean hasParent(Resource #{variables[0]}, Resource #{variables[1]})")
-    else
-      if transduction.match(/\/\*\*[^E]*Either:.*Or:/m) or transduction.match(/\/\*\*[^A]*Ambiguous label\./) then
-        transduction.sub!(/public static /, 'public static Set<Resource> ')
+    if line.match('http://') then
+      if line.match(/http:\/\/[^'")]+#[^'")]+/) then
+        namespace = line.scan(/http:\/\/[^'")]+/)[0].sub(/(#).*$/, '\1') unless namespace
       else
-        transduction.sub!(/public static /, 'public static Resource ')
+        namespace = line.scan(/http:\/\/[^'")]+/)[0].sub(/\/[^\/]+$/, '/') unless namespace
+      end
+      if line.match("#{namespace}\w+") then
+        line.gsub!(namespace, '') unless line.strip.start_with?('#')
       end
     end
-    transduction << '()' unless transduction.end_with?(")")
-    transduction << ' {'
-  elsif line.strip.start_with?('#') then
-    unless comment then
-      comment = line.strip.sub(/^# ?/, ' ')
+
+    if line.start_with?('class') then
+      java_class = line.sub(/^.* /, '')
+      transduction = "public class #{java_class} {"
+    elsif line.strip.start_with?('def ') then
+      leading_spaces = line.gsub(/[^ ].*$/, '')
+      transduction = ''
+      if comment then
+        transduction << "#{("/**\n *" + comment).gsub(/^/, "#{leading_spaces}")}\n#{leading_spaces} */\n"
+        comment = nil
+      end
+      transduction << "  public static #{line.sub('?', '').sub(/self\./, '').sub(/ *def\ /, '')}"
+      method_name = transduction.sub(/^.*public static /m, '').sub(/(\(.*)?$/, '')
+      transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode|byte|char|short|int|long|float|double|boolean)$/)
+      variables = transduction.scan(/^\s*public static \w+\((.+)\)$/)
+      variables = variables[0][0].split(',').map { |variable| variable.strip } if variables.length > 0
+      if method_name == 'is_object_property' then
+        transduction.sub!(/public static .*$/, "public static boolean isObjectProperty(Resource #{variables[0]})")
+      elsif method_name == 'is_datatype_property' then
+        transduction.sub!(/public static .*$/, "public static boolean isDatatypeProperty(Resource #{variables[0]})")
+      elsif method_name == 'is_class' then
+        transduction.sub!(/public static .*$/, "public static boolean isClass(Resource #{variables[0]})")
+      elsif method_name == 'is_named_individual' then
+        transduction.sub!(/public static .*$/, "public static boolean isNamedIndividual(Resource #{variables[0]})")
+      elsif method_name == 'with_parent' then
+        transduction.sub!(/public static .*$/, "public static Set<Resource> withParent(Set<Resource> #{variables[0]}, final Resource #{variables[1]})")
+      elsif method_name == 'has_parent' then
+        transduction.sub!(/public static .*$/, "public static boolean hasParent(Resource #{variables[0]}, Resource #{variables[1]})")
+      else
+        if transduction.match(/\/\*\*[^E]*Either:.*Or:/m) or transduction.match(/\/\*\*[^A]*Ambiguous label\./) then
+          transduction.sub!(/public static /, 'public static Set<Resource> ')
+        else
+          transduction.sub!(/public static /, 'public static Resource ')
+        end
+      end
+      transduction << '()' unless transduction.end_with?(")")
+      transduction << ' {'
+    elsif line.strip.start_with?('#') then
+      unless comment then
+        comment = line.strip.sub(/^# ?/, ' ')
+      else
+        comment << "\n#{line.strip.gsub(/^# ?/, ' * ').gsub(/\+([^+]+)\+::/, '@param \1')}"
+      end
+      transduction = nil
+    elsif line.strip.start_with?('end') then
+      if class_closed then
+        transduction = nil
+      else
+        if line.start_with?('end') then
+          class_closed = true
+          cls.gsub!(/_namespace_#{java_class}\(/, 'return ResourceFactory.createResource(') unless namespace_wrapper_generated
+        end
+        transduction = line.sub(/end/, '}')
+      end
+    elsif line.strip.start_with?('if ') or line.strip.start_with?('elsif') then
+      transduction = "#{line.sub(/ then$/, '').sub('elsif', 'else if').gsub('@@', '__').gsub(/RDF::URI\.new\(([^)]+)\)/, "_namespace_#{java_class}(\\1)").gsub(/(\w)\?\(/, '\1(')}".gsub(/\.has_key\(([^)]+)\)/, '.containsKey(\1)').gsub(/\[([^\]]+)\]/, '.get(\1)')
+      if transduction.match(/if ([^=]+|_namespace_[^=]+) ?== ?([^_].*|_namespace_.*)/)
+        transduction.sub!(/if ([^= ]+) ?== ?(\S+)\s+$/, 'if \1.equals(\2)')
+        transduction.sub!(/_namespace_\w+\('(\w+)'\)/, "\"#{namespace}\\1\"")
+      end
+      transduction.sub!(/\.equals\(("[^"]+")\)/, '.equals(ResourceFactory.createResource(\1))')
+      transduction.sub!(/if /, 'if (')
+      transduction.sub!(/$/, ') {')
+    elsif line.strip.start_with?('return [') then
+      transduction = line.sub(/return \[/, 'return new HashSet<Resource>(Arrays.asList(new Resource[] {').sub(/\]$/, '}));').gsub(/RDF::URI\.new\(([^)]+)\)/, "_namespace_#{java_class}(\\1)")
+    elsif line.strip.start_with?('private') then
+      private_scope = true
+      namespace_wrapper_generated = true
+      transduction = "  private static Resource _namespace_#{java_class}(String accession) {\n"
+      transduction << "    if (isClass(ResourceFactory.createResource(\"#{namespace}\" + accession))) {\n"
+      transduction << "      return ResourceFactory.createResource(\"#{namespace}\" + accession);\n"
+      transduction << "    } else {\n"
+      transduction << "      return ResourceFactory.createProperty(\"#{namespace}\" + accession);\n"
+      transduction << "    }\n"
+      transduction << "  }\n\n"
     else
-      comment << "\n#{line.strip.gsub(/^# ?/, ' * ').gsub(/\+([^+]+)\+::/, '@param \1')}"
+      transduction = line.gsub('@@', '__').gsub(/RDF::URI\.new\(([^)]+)\)/, "_namespace_#{java_class}(\\1)").gsub(/(\w+)\.select ?\{ ?\|(\w+)\| ?(.*[^ ]) ?\}/, 'new HashSet<Resource>(CollectionUtils.select(\1, new Predicate() { public boolean evaluate(Object \2) { return \3; } }))').gsub(/(\w)\?\(/, '\1(').gsub('has_parent(', 'hasParent((Resource)').gsub(/\[([^\]]+)\]/, '.get(\1)')
+      transduction.gsub!('__', '__') unless line.strip.start_with?('@@')
+      transduction << ';' unless line.strip.empty?
     end
-    transduction = nil
-  elsif line.strip.start_with?('end') then
-    transduction = line.sub(/end/, '}')
-  elsif line.strip.start_with?('if ') or line.strip.start_with?('elsif') then
-    transduction = "#{line.sub(/ then$/, '').sub('elsif', 'else if').gsub('@@', '__').gsub(/RDF::URI\.new\(([^)]+)\)/, "_namespace_#{java_class}(\\1)").gsub(/(\w)\?\(/, '\1(')}".gsub(/\.has_key\(([^)]+)\)/, '.containsKey(\1)').gsub(/\[([^\]]+)\]/, '.get(\1)')
-    if transduction.match(/if ([^=]+|_namespace_[^=]+) ?== ?([^_].*|_namespace_.*)/)
-      transduction.sub!(/if ([^= ]+) ?== ?(\S+)\s+$/, 'if \1.equals(\2)')
-      transduction.sub!(/_namespace_\w+\('(\w+)'\)/, "\"#{namespace}\\1\"")
+
+    if transduction and transduction.strip.start_with?('__') then
+      variable = transduction.scan(/__\w+/)[0]
+      map = {}
+      map = Hash[*transduction.sub(/^.* \{/, '').sub(/\};/, '').split(',').map { |assignment| assignment.split('=>').map { |kv| kv.strip } }.flatten.map { |function| if function.match(/'\w+'/) then "#{namespace}#{function.scan(/'\w+'/)[0].gsub(/'/, '')}" else nil end }.compact ] if transduction.match(/\{\s*\S+.*\}/)
+      transduction = "  private static Map<Resource, Resource> #{variable} = _init_#{variable}();\n\n"
+      transduction << "  private static Map<Resource, Resource> _init_#{variable}() {\n"
+      transduction << "    Map<Resource, Resource> map = new HashMap<Resource, Resource>();\n\n"
+      map.each_pair { |key, value| transduction << "    map.put(ResourceFactory.createResource(\"#{key}\"), ResourceFactory.createResource(\"#{value}\"));\n" }
+      transduction << "\n"
+      transduction << "    return map;\n"
+      transduction << "  }\n"
     end
-    transduction.sub!(/\.equals\(("[^"]+")\)/, '.equals(ResourceFactory.createResource(\1))')
-    transduction.sub!(/if /, 'if (')
-    transduction.sub!(/$/, ') {')
-  elsif line.strip.start_with?('return [') then
-    transduction = line.sub(/return \[/, 'return new HashSet<Resource>(Arrays.asList(new Resource[] {').sub(/\]$/, '}));').gsub(/RDF::URI\.new\(([^)]+)\)/, "_namespace_#{java_class}(\\1)")
-  elsif line.strip.start_with?('private') then
-    private_scope = true
-    transduction = "  private static Resource _namespace_#{java_class}(String accession) {\n"
-    transduction << "    if (isClass(ResourceFactory.createResource(\"#{namespace}\" + accession))) {\n"
-    transduction << "      return ResourceFactory.createResource(\"#{namespace}\" + accession);\n"
-    transduction << "    } else {\n"
-    transduction << "      return ResourceFactory.createProperty(\"#{namespace}\" + accession);\n"
-    transduction << "    }\n"
-    transduction << "  }\n\n"
-  else
-    transduction = line.gsub('@@', '__').gsub(/RDF::URI\.new\(([^)]+)\)/, "_namespace_#{java_class}(\\1)").gsub(/(\w+)\.select ?\{ ?\|(\w+)\| ?(.*[^ ]) ?\}/, 'new HashSet<Resource>(CollectionUtils.select(\1, new Predicate() { public boolean evaluate(Object \2) { return \3; } }))').gsub(/(\w)\?\(/, '\1(').gsub('has_parent(', 'hasParent((Resource)').gsub(/\[([^\]]+)\]/, '.get(\1)')
-    transduction.gsub!('__', '__') unless line.strip.start_with?('@@')
-    transduction << ';' unless line.strip.empty?
-  end
 
-  if transduction and transduction.strip.start_with?('__') then
-    variable = transduction.scan(/__\w+/)[0]
-    map = {}
-    map = Hash[*transduction.sub(/^.* \{/, '').sub(/\};/, '').split(',').map { |assignment| assignment.split('=>').map { |kv| kv.strip } }.flatten.map { |function| if function.match(/'\w+'/) then "#{namespace}#{function.scan(/'\w+'/)[0].gsub(/'/, '')}" else nil end }.compact ] if transduction.match(/\{\s*\S+.*\}/)
-    transduction = "  private static Map<Resource, Resource> #{variable} = _init_#{variable}();\n\n"
-    transduction << "  private static Map<Resource, Resource> _init_#{variable}() {\n"
-    transduction << "    Map<Resource, Resource> map = new HashMap<Resource, Resource>();\n\n"
-    map.each_pair { |key, value| transduction << "    map.put(ResourceFactory.createResource(\"#{key}\"), ResourceFactory.createResource(\"#{value}\"));\n" }
-    transduction << "\n"
-    transduction << "    return map;\n"
-    transduction << "  }\n"
-  end
+    cls << "#{transduction}\n".gsub(/'/, '"') if transduction
+  }
+
+  cls
+end
 
-  cls << "#{transduction}\n".gsub(/'/, '"') if transduction
+unless @loaded_externally then
+  namespace = nil
 
-}
+  if ARGV.length == 1 then
+    namespace = ARGV[0]
+  end
 
-puts cls
+  puts javaify(STDIN, namespace)
+end