rbbt-text 0.6.0 → 0.6.2

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Files changed (5) hide show
  1. data/lib/rbbt/corpus/corpus.rb +2 -0
  2. data/lib/rbbt/nlp/nlp.rb +2 -2
  3. data/share/install/software/ChemicalTagger +6 -5
  4. data/test/rbbt/ner/test_chemical_tagger.rb +1 -1
  5. metadata +6 -6
data/lib/rbbt/corpus/corpus.rb CHANGED
@@ -34,10 +34,12 @@ class Corpus
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  def document(namespace, id, type, hash)
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  docid = [namespace, id, type, hash] * ":"
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+ raise "Document '#{ docid }' was not found." unless @document_repo.include? docid
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  Document.new(persistence_for(docid), docid, @document_repo[docid], @global_annotations)
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  end
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  def docid(docid)
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+ raise "Document '#{ docid }' was not found." unless @document_repo.include? docid
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  Document.new(persistence_for(docid), docid, @document_repo[docid], @global_annotations)
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  end
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data/lib/rbbt/nlp/nlp.rb CHANGED
@@ -16,10 +16,10 @@ module NLP
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  #Rbbt.software.opt.StanfordParser.define_as_install Rbbt.share.install.software.StanfordParser.find
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  #Rbbt.software.opt.StanfordParser.produce
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- Rbbt.software.opt.Geniass.define_as_install Rbbt.share.install.software.Geniass.find
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+ Rbbt.claim Rbbt.software.opt.Geniass, :install, Rbbt.share.install.software.Geniass.find
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  Rbbt.software.opt.Geniass.produce
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- Rbbt.software.opt.Gdep.define_as_install Rbbt.share.install.software.Gdep.find
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+ Rbbt.claim Rbbt.software.opt.Gdep, :install, Rbbt.share.install.software.Gdep.find
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  Rbbt.software.opt.Gdep.produce
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  NEW_LINE_MASK = "\t\t \t \t"
data/share/install/software/ChemicalTagger CHANGED
@@ -5,7 +5,7 @@ RBBT_SOFTWARE_DIR="$2"
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  source "$INSTALL_HELPER_FILE"
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  name='ChemicalTagger'
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- url="https://bitbucket.org/lh359/chemicaltagger/downloads/chemicalTagger-1.0-jar-with-dependencies.jar"
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+ url="https://bitbucket.org/wwmm/chemicaltagger/downloads/chemicalTagger-1.0.2-jar-with-dependencies.jar"
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  PKG_DIR=`opt_dir $name`
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  [ -d $PKG_DIR ] || mkdir -p $PKG_DIR
@@ -41,12 +41,14 @@ class RbbtChemicalTagger{
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  ArrayList tokens = new ArrayList();
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  ArrayList molecules = new ArrayList();
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  ArrayList new_tokens = new ArrayList();
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+
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  tokens.add(tree);
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  while (tokens.size() > 0){
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  for(int tree_i = 0; tree_i < tokens.size(); tree_i++){
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  Tree subtree = (Tree) tokens.get(tree_i);
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  int type = subtree.getType();
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- if (type == 78){
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+
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+ if (type == 84){
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  molecules.add(subtree.getChild(0));
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  }else{
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  for(int tree_j = 0; tree_j < subtree.getChildCount(); tree_j++){
@@ -75,7 +77,6 @@ class RbbtChemicalTagger{
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  EOF
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- env |grep JAVA
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-
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+ env | grep JAVA
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- (env CLASSPATH="$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 $PKG_DIR)
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+ (env CLASSPATH="$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 CHANGED
@@ -10,7 +10,7 @@ class TestChemicalTagger < Test::Unit::TestCase
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  ner = ChemicalTagger.new
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  str = "Alternatively, rearrangement of O-(w-haloalkyl)esters 34 of 2-carboethoxy-N-hydroxypyridine-2-selone affords azonianaphthalenium halides 37 in 79% yield"
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  mentions = ner.match(str, "CM", false)
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-
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+
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  good_mentions = ["2-carboethoxy-N-hydroxypyridine-2-selone", "O-(w-haloalkyl)esters"]
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  good_mentions.each{|mention|
metadata CHANGED
@@ -1,13 +1,13 @@
1
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  --- !ruby/object:Gem::Specification
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  name: rbbt-text
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  version: !ruby/object:Gem::Version
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- hash: 7
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- prerelease: false
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+ hash: 3
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+ prerelease:
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  segments:
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  - 0
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  - 6
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- - 0
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- version: 0.6.0
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+ - 2
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+ version: 0.6.2
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  platform: ruby
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  authors:
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  - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-09-07 00:00:00 +02:00
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+ date: 2011-10-03 00:00:00 +02:00
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  default_executable: get_ppis.rb
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -191,7 +191,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.3.7
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+ rubygems_version: 1.6.2
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  signing_key:
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  specification_version: 3
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  summary: Text mining tools for the Ruby Bioinformatics Toolkit (rbbt)