rbbt-text 0.6.0 → 0.6.2

data/lib/rbbt/corpus/corpus.rb

@@ -34,10 +34,12 @@ class Corpus
 
   def document(namespace, id, type, hash)
     docid = [namespace, id, type, hash] * ":"
+    raise "Document '#{ docid }' was not found." unless @document_repo.include? docid
     Document.new(persistence_for(docid), docid, @document_repo[docid], @global_annotations)
   end
 
   def docid(docid)
+    raise "Document '#{ docid }' was not found." unless @document_repo.include? docid
     Document.new(persistence_for(docid), docid, @document_repo[docid], @global_annotations)
   end
 

data/lib/rbbt/nlp/nlp.rb

@@ -16,10 +16,10 @@ module NLP
   #Rbbt.software.opt.StanfordParser.define_as_install Rbbt.share.install.software.StanfordParser.find
   #Rbbt.software.opt.StanfordParser.produce
 
-  Rbbt.software.opt.Geniass.define_as_install Rbbt.share.install.software.Geniass.find
+  Rbbt.claim Rbbt.software.opt.Geniass, :install, Rbbt.share.install.software.Geniass.find
   Rbbt.software.opt.Geniass.produce
 
-  Rbbt.software.opt.Gdep.define_as_install Rbbt.share.install.software.Gdep.find
+  Rbbt.claim Rbbt.software.opt.Gdep, :install, Rbbt.share.install.software.Gdep.find
   Rbbt.software.opt.Gdep.produce
 
   NEW_LINE_MASK = "\t\t \t  \t"

data/share/install/software/ChemicalTagger

@@ -5,7 +5,7 @@ RBBT_SOFTWARE_DIR="$2"
 source "$INSTALL_HELPER_FILE"
 
 name='ChemicalTagger'
-url="https://bitbucket.org/lh359/chemicaltagger/downloads/chemicalTagger-1.0-jar-with-dependencies.jar"
+url="https://bitbucket.org/wwmm/chemicaltagger/downloads/chemicalTagger-1.0.2-jar-with-dependencies.jar"
 
 PKG_DIR=`opt_dir $name`
 [ -d $PKG_DIR ] || mkdir -p $PKG_DIR
@@ -41,12 +41,14 @@ class RbbtChemicalTagger{
         ArrayList tokens = new ArrayList();
         ArrayList molecules = new ArrayList();
         ArrayList new_tokens = new ArrayList();
+
         tokens.add(tree);
         while (tokens.size() > 0){
             for(int tree_i = 0; tree_i < tokens.size(); tree_i++){
                 Tree subtree = (Tree) tokens.get(tree_i);
                 int type = subtree.getType();
-                if (type == 78){
+
+                if (type == 84){
                     molecules.add(subtree.getChild(0));
                 }else{
                     for(int tree_j = 0; tree_j < subtree.getChildCount(); tree_j++){
@@ -75,7 +77,6 @@ class RbbtChemicalTagger{
 
 EOF
 
-env |grep JAVA
-
+env | grep JAVA
 
-(env CLASSPATH="$OPT_JAR_DIR/ChemicalTagger.jar:$CLASSPATH" /home/mvazquezg/software/opt/java/jdk/bin/javac /tmp/RbbtChemicalTagger.java && jar uf "$PKG_DIR/ChemicalTagger.jar" -C /tmp RbbtChemicalTagger.class) || (rm "$PKG_DIR/ChemicalTagger.jar" && rmdir $PKG_DIR)
+(env CLASSPATH="$OPT_JAR_DIR/ChemicalTagger.jar:$CLASSPATH" javac /tmp/RbbtChemicalTagger.java && jar uf "$PKG_DIR/ChemicalTagger.jar" -C /tmp RbbtChemicalTagger.class) || (rm "$PKG_DIR/ChemicalTagger.jar" && rmdir $PKG_DIR)

data/test/rbbt/ner/test_chemical_tagger.rb

@@ -10,7 +10,7 @@ class TestChemicalTagger < Test::Unit::TestCase
       ner = ChemicalTagger.new
       str  = "Alternatively, rearrangement of O-(w-haloalkyl)esters 34 of 2-carboethoxy-N-hydroxypyridine-2-selone affords azonianaphthalenium halides 37 in 79% yield"
       mentions = ner.match(str, "CM", false)
-      
+
       good_mentions = ["2-carboethoxy-N-hydroxypyridine-2-selone", "O-(w-haloalkyl)esters"]
 
       good_mentions.each{|mention| 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-text
 version: !ruby/object:Gem::Version 
-  hash: 7
-  prerelease: false
+  hash: 3
+  prerelease: 
   segments: 
   - 0
   - 6
-  - 0
-  version: 0.6.0
+  - 2
+  version: 0.6.2
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-07 00:00:00 +02:00
+date: 2011-10-03 00:00:00 +02:00
 default_executable: get_ppis.rb
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -191,7 +191,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: Text mining tools for the Ruby Bioinformatics Toolkit (rbbt)