rbbt 1.1.0 → 1.1.1

data/README.rdoc

@@ -79,8 +79,8 @@ Install the gem normally <tt>gem install rbbt</tt>. The gem includes a configura
 
 === Using rbbt to translate identifiers
 
-1. Do <tt>rbbt_config install identifiers</tt> to do deploy the configuration files and download entrez data, this needs to be done just once.
-3. Now you may do <tt>rbbt_config update organisms</tt> toprocess all the organisms, or <tt>rbbt_config update organisms -o sgd</tt> to process only yeast (sgd).
+1. Do <tt>rbbt_config prepare identifiers</tt> to do deploy the configuration files and download entrez data, this needs to be done just once.
+3. Now you may do <tt>rbbt_config install organisms</tt> toprocess all the organisms, or <tt>rbbt_config install organisms -o sgd</tt> to process only yeast (sgd).
 4. You may now use a script like this to translate gene identifiers from yeast feed from the standard input
   require 'rbbt/sources/organism'
 
@@ -92,12 +92,12 @@ Install the gem normally <tt>gem install rbbt</tt>. The gem includes a configura
 
 First prepare the organisms as you did in the previous section. Next, if you want to use the default NER module:
 
-1. Install the Biocreative data used to train the model and compile the CRF++ plugin, <tt>rbbt_config install rner</tt>. You may need at this point to install ParseTree and ruby2ruby
-2. Build the module for a particular organism <tt>rbbt_config update ner -o sgd</tt>. You need to have the gems ParseTree and ruby2ruby for this to work. This process can take a long time.
+1. Install the Biocreative data used to train the model and compile the CRF++ plugin, <tt>rbbt_config prepare rner</tt>. You may need at this point to install ParseTree and ruby2ruby
+2. Build the module for a particular organism <tt>rbbt_config install ner -o sgd</tt>. You need to have the gems ParseTree and ruby2ruby for this to work. This process can take a long time.
 
 Or, if you wan to use Abner or Banner:
 
-1. Download and install the packages <tt>rbbt_config install java_ner</tt> 
+1. Download and install the packages <tt>rbbt_config prepare java_ner</tt> 
 
 You may now, for example, find mentions to genes in articles from a PubMed query using this script
 
@@ -123,7 +123,7 @@ You may now, for example, find mentions to genes in articles from a PubMed query
 
 This is the complete list of gem requirements: <tt>ParseTree ruby2ruby simpleconsole rjb rsruby stemmer rand rake progress-monitor</tt>. Some of these gems to not work with ruby 1.9 at the time, or may be a bit more complicated to install, for that reason *they are not reported as dependencies and are only required when they are about to be used*. Note that some of these gems are in the gemcutter repository, you may need to install the <tt>gemcutter</tt> gem and do <tt>gem tumble</tt>
 
-Some of the API requires to have some data processed using rbbt_config. This command is used to install third party software, download data from the internet, or build models. The command <tt>rbbt_config install all</tt> will install and process everything, this will take a long time, specially building the NER models. So you might want to start with the basic install and include more things as they are needed. 
+Some of the API requires to have some data processed using rbbt_config. This command is used to install third party software, download data from the internet, or build models. The command <tt>rbbt_config prepare all</tt> will install and process everything, this will take a long time, specially building the NER models. So you might want to start with the basic install and include more things as they are needed. 
 
 
 = Note on Patches/Pull Requests

data/bin/rbbt_config

@@ -15,13 +15,13 @@ end
 TASKS= %w(organisms ner norm classifier biocreative entrez go wordlists polysearch abner banner crf++)
 
 $USAGE =<<EOT
-#{__FILE__} <action> [<subaction>] [--force] [--organism <org>]
+#{__FILE__} <action> [<subaction>] [--update] [--organism <org>]
 
   actions:
 
     * configure:   Set paths for data, cache, and tmp directories
 
-    * install:
+    * prepare:
       
       Basic subactions:
       
@@ -50,12 +50,12 @@ $USAGE =<<EOT
       * classifier:   organisms, wordlists, classifier, go
       * all:          #{TASKS.join(", ")}
 
-    * update: 
+    * install: 
       * organisms:      Gather organisms data
       * ner:            Build Named Entity Recognition Models. Mention Normalization needs no training.
       * classification: Build Function/Process Classifiers
 
-      --force:          Rebuild models or reprocess organism data even if present. You may want to purge the cache 
+      --update:         Rebuild models or reprocess organism data even if present. You may want to purge the cache 
                         to be up to date with the data in the internet.
 
       --organism:       Gather data only for that particular organism. The organism must be specified by the 
@@ -74,7 +74,7 @@ EOT
 
 class Controller < SimpleConsole::Controller
 
-  params :bool => {:f => :force},
+  params :bool => {:u => :update},
          :string => {:o => :organism}
 
   def organisms
@@ -89,7 +89,7 @@ class Controller < SimpleConsole::Controller
     render :action => :usage
   end
 
-  def update
+  def install
     raise "Run #{__FILE__} configure first to configure rbbt" if $noconfig
 
     case params[:id]
@@ -103,12 +103,12 @@ class Controller < SimpleConsole::Controller
       redirect_to :action => :help, :id => :update
     end
 
-    $force = true if params[:force]
+    $force = true if params[:update]
     $org = params[:organism] if params[:organism]
 
   end
 
-  def install
+  def prepare
     raise "Run #{__FILE__} configure first to configure rbbt" if $noconfig
     case params[:id]
     when "identifiers"
@@ -146,7 +146,7 @@ class Controller < SimpleConsole::Controller
       @tasks = [params[:id]]
     end
 
-    $force = true if params[:force]
+    $force = true if params[:update]
     $org = params[:organism] if params[:organism]
 
   end
@@ -175,7 +175,7 @@ class View < SimpleConsole::View
   end
 
 
-  def install
+  def prepare
     load File.join(Rbbt.rootdir, 'tasks/install.rake')
 
     @tasks.each{|t|
@@ -184,7 +184,7 @@ class View < SimpleConsole::View
     }
   end
 
-  def update
+  def install
 
     puts "Changing directory to #{@location}"
     chdir @location

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt
 version: !ruby/object:Gem::Version 
-  version: 1.1.0
+  version: 1.1.1
 platform: ruby
 authors: 
 - Miguel Vazquez