abstractor 1.0.9 → 1.0.10

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data/README.md

@@ -46,6 +46,10 @@ Add abstractor to your Gemfile:
 
   gem 'abstractor'
 
+Also add the paper\_trail gem to your Gemfile (if it is not already there):
+
+  gem 'paper_trail'
+
 Bundle, install, and migrate:
 
 * bundle install

data/lib/abstractor/version.rb

@@ -1,3 +1,3 @@
 module Abstractor
-  VERSION = '1.0.9'
+  VERSION = '1.0.10'
 end

data/lib/generators/abstractor/install/install_generator.rb

@@ -9,6 +9,7 @@ module Abstractor
     class_option "customize-helpers", :type => :boolean
     class_option "customize-layout", :type => :boolean
     class_option "current-user-helper", :type => :string
+    class_option "install-stanford-core-nlp", :type => :boolean
 
     def self.source_paths
       paths = self.superclass.source_paths
@@ -52,6 +53,21 @@ module Abstractor
       end
     end
 
+    def setup_stanford_core_nlp
+      unless options["install-stanford-core-nlp"]
+        puts "Running rake abstractor:setup:stanford_core_nlp"
+        puts 'Please be patient...this could take a while'
+        `rake abstractor:setup:stanford_core_nlp`
+
+        insert_into_file("#{Rails.root}/config/environments/development.rb", :after => /::Application.configure do\n/) do
+'  StanfordCoreNLP.use :english
+  StanfordCoreNLP.jar_path = "#{Rails.root}/lib/stanford-core-nlp/"
+  StanfordCoreNLP.model_path = "#{Rails.root}/lib/stanford-core-nlp/"
+'
+        end
+      end
+    end
+
     def make_customizable
       if options["customize-all"] || options["customize-controllers"]
         path = "#{Rails.root}/app/controllers/abstractor"

data/lib/tasks/abstractor_tasks.rake

@@ -1,22 +1,38 @@
-# desc "Explaining what the task does"
-# task :abstractor do
-#   # Task goes here
-# end
+require 'open-uri'
+require 'zip'
 
 namespace :abstractor do
   namespace :setup do
-    desc 'Load abstraction schemas (specify file to parse with FILE=myfile.yml) '
-    task :abstraction_schemas => :environment do
-      file = ENV["FILE"]
-      raise "File name has to be provided" if file.blank?
-      raise "File does not exist: #{file}" unless FileTest.exists?(file)
-      puts 'Little my says not done yet!  Get to work!'
-    end
-
-    desc 'Load '
+    desc 'Load abstractor system tables'
     task :system => :environment do
-      # raise "File does not exist: #{file}" unless FileTest.exists?(file)
       Abstractor::Setup.system
     end
+
+    desc "Setup Stanford CoreNLP library in lib/stanford-core-nlp directory"
+    task :stanford_core_nlp => :environment do
+      directory = "#{Rails.root}/lib/stanford-core-nlp/"
+      Dir.mkdir(directory) unless File.exists?(directory)
+      puts 'Please be patient...This could take a while.'
+      file = "#{Rails.root}/lib/stanford-core-nlp/stanford-core-nlp-minimal.zip"
+      open(file, 'wb') do |fo|
+        fo.print open('http://louismullie.com/treat/stanford-core-nlp-minimal.zip').read
+      end
+
+      file = "#{Rails.root}/lib/stanford-core-nlp/stanford-core-nlp-minimal.zip"
+      destination = "#{Rails.root}/lib/stanford-core-nlp/"
+      puts 'Unzipping...'
+      unzip_file(file, destination)
+    end
   end
+
+  private
+    def unzip_file (file, destination)
+      Zip::File.open(file) { |zip_file|
+       zip_file.each { |f|
+         f_path=File.join(destination, f.name)
+         FileUtils.mkdir_p(File.dirname(f_path))
+         zip_file.extract(f, f_path) unless File.exist?(f_path)
+       }
+      }
+    end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: abstractor
 version: !ruby/object:Gem::Version
-  version: 1.0.9
+  version: 1.0.10
 platform: ruby
 authors:
 - Michael Gurley, Yulia Bushmanova
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-06 00:00:00.000000000 Z
+date: 2014-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -144,6 +144,20 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.5.1
+- !ruby/object:Gem::Dependency
+  name: rubyzip
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
@@ -385,8 +399,8 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 3.1.1
 description: A Rails engine gem for deriving discrete data points from narrative text
-  via natural language processing.  The gem includes a user interface to present the
-  abstracted data points for confirmation/revision by curator.
+  via natural language processing (NLP).  The gem includes a user interface to present
+  the abstracted data points for confirmation/revision by curator.
 email:
 - michaeljamesgurley@gmail.com, y.bushmanova@gmail.com
 executables: []
@@ -521,7 +535,6 @@ files:
 - lib/generators/abstractor/install/templates/controllers/abstractor_abstraction_groups_controller.rb
 - lib/generators/abstractor/install/templates/controllers/abstractor_abstractions_controller.rb
 - lib/generators/abstractor/install/templates/controllers/abstractor_suggestions_controller.rb
-- lib/generators/abstractor/install/templates/dictionaries.yml
 - lib/generators/abstractor/install/templates/helpers/abstractions_helper.rb
 - lib/generators/abstractor/install/templates/models/abstractor_abstraction.rb
 - lib/generators/abstractor/install/templates/models/abstractor_abstraction_group.rb
@@ -737,7 +750,7 @@ files:
 - lib/setup/data/site_site_categories.txt
 - lib/tasks/abstractor_tasks.rake
 - lib/tasks/cucumber.rake
-homepage: 
+homepage: http://github.com/nubic/abstractor
 licenses:
 - MIT
 metadata: {}
@@ -761,6 +774,6 @@ rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: A Rails engine gem for deriving discrete data points from narrative text
-  via natural language processing.  The gem includes a user interface to present the
-  abstracted data points for confirmation/revision by curator.
+  via natural language processing (NLP).  The gem includes a user interface to present
+  the abstracted data points for confirmation/revision by curator.
 test_files: []

data/lib/generators/abstractor/install/templates/dictionaries.yml

@@ -1,235 +0,0 @@
-# ---- General structure:
-#   :dictionaries:
-#    - :name: string                                                            # has to be unique within not-deleted dictionaries
-#      :parameter_categories:
-#       - :name: string                                                         # has to be unique within the dictionary
-#         :parameters:
-#           - :name: string                                                     # used for display
-#             :unique_identifier:                                               # has to be unique within the dictionary
-#             :export:
-#               :model                                                          # name of the model to be used for exporting
-#               :method                                                         # name of the model method to be used for exporting
-#             :search:                                                          # parameter search model and method combination has to be unique within the category
-#               :model: string                                                  # name of the model to be used for searching
-#               :method: string                                                 # name of the model method to be used for searching
-#               :parameter_type: numeric/date/list/combobox/text/string         # used to define applicable operators/display options. does not have to be restricted to the given list, but additional parameters will require adding operators to match
-#               :parameter_value_categories_source:                             # used to define parameter value categories
-#                 :model: string                                                # source model to be used to load parameter value categiories
-#                 :method: string                                               # method in the source model that returns parameter_value_categories in a form of [{:name => 'string, :unique_identifier => 'adventure', :display_order => 1, :collapse => true}]
-#               :parameter_value_categories:                                    # used to define parameter value categories
-#                 - :name: string
-#                   :unique_identifier: string                                  # has to be unique within parameter
-#                   :collapse: boolean                                          # used to define if parameter category should be collapsed in the list and its values hidden from the view
-#                   :display_order: integer
-#               :parameter_values:                                              # needs to be defined for list/combobox parameters unless parameter values come from the model, see ':source'
-#                 - :name: string                                               # used for display, if not provided, 'search_value' will be used instead
-#                   :search_value: string                                       # has to be unique within parameter, intendend to be used as a database value while searching
-#                   :parameter_value_category: string                           # used to define category for parameter value, should match one of parameter_value_categories unique_identifiers listed above
-#               :source:
-#                 :model: string                                                # source model to be used to load parameter values
-#                 :method: string                                               # method/method in the source model to be used to load parameter values
-
----
-:dictionaries:
-  - :name: Sample dictionary
-    :parameter_categories:
-      - :name: Demographic criteria
-        :parameters:
-          - :name: Age at case collection date
-            :unique_identifier: age_at_case_collect
-            :search:
-              :model: Patient
-              :method: age_at_case_collect
-              :parameter_type: numeric
-
-          - :name: Age based on current date
-            :unique_identifier: age_based_on_current_date
-            :export:
-              :model: Patient
-              :method: age_based_on_current_date
-
-          - :name: Date of birth
-            :unique_identifier: birth_dt_tm
-            :search:
-              :model: Patient
-              :method: birth_dt_tm
-              :parameter_type: date
-            :export:
-              :model: Patient
-              :method: age_based_on_current_date
-
-          - :name: Ethnic group
-            :unique_identifier: ethnic_grp
-            :search:
-              :model: Patient
-              :method: ethnic_grp
-              :parameter_type: combobox
-              :parameter_values:
-                - :name: Hispanic or Latino
-                  :search_value: hisp_or_latino
-                - :name: NOT Hispanic or Latino
-                  :search_value: not_hisp_or_latino
-                - :name: Unable to answer
-                  :search_value: unknown
-                - :name: Declined to answer
-                  :search_value: declined
-
-          - :name: Consented
-            :unique_identifier: surg_inpatient_mortality
-            :search:
-              :model: Surgery
-              :method: consented
-              :parameter_type: list
-              :parameter_values:
-                - :search_value: yes
-                - :search_value: no
-
-          - :name: Gender
-            :unique_identifier: sex
-            :search:
-              :model: Patient
-              :method: sex
-              :parameter_type: list
-              :parameter_values:
-                - :name: Male
-                  :search_value: male
-                - :name: Female
-                  :search_value: female
-                - :name: Indeterminent
-                  :search_value: indeterminent
-                - :name: Unknown
-                  :search_value: unknown
-                - :name: Unspecified
-                  :search_value: uncpecified
-            :export:
-              :model: Patient
-              :method: gender
-
-          - :name: Race
-            :exclusive: false
-            :unique_identifier: race
-            :search:
-              :model: Patient
-              :method: race
-              :parameter_type: combobox
-              :parameter_values:
-                - :search_value: American Indian or Alaska Native
-                - :search_value: Asian
-                - :search_value: Black or African American
-                - :search_value: Hispanic or Latino
-                - :search_value: Native Hawaiian or Other Pacific Islander
-                - :search_value: White or Caucasian
-                - :search_value: Other
-                - :search_value: Declined to answer
-                - :search_value: Unable to answer
-            :export:
-              :model: Patient
-              :method: race
-
-      - :name: Case criteria
-        :parameters:
-          - :name: Accession date
-            :unique_identifier: accessioned_dt_tm
-            :search:
-              :model: Case
-              :method: accessioned_dt_tm
-              :parameter_type: date
-
-          - :name: Text search diagnosis
-            :exclusive: false
-            :unique_identifier: case_specimen_diagnosis
-            :search:
-              :model: Case
-              :method: case_specimen_diagnosis
-              :parameter_type: text
-
-  - :name: Librarian dictionary
-    :parameter_categories:
-      - :name: By author
-        :parameters:
-          - :name: "Last name"
-            :unique_identifier: autor_last_name
-            :search:
-              :model: Author
-              :method: autor_last_name
-              :parameter_type: string
-
-          - :name: "First name"
-            :unique_identifier: autor_first_name
-            :search:
-              :model: Author
-              :method: autor_first_name
-              :parameter_type: text
-
-          - :name: "Country"
-            :unique_identifier: country
-            :search:
-              :model: Author
-              :method: country
-              :parameter_type: text
-
-          - :name: "Type"
-            :unique_identifier: author_type
-            :search:
-              :model: Book
-              :method: type
-              :parameter_type: list
-              :parameter_values:
-                - :search_value: author
-                - :search_value: co-author
-                - :search_value: reviewer
-      - :name: Book criteria
-        :parameters:
-          - :name: "Type"
-            :unique_identifier: book_type
-            :search:
-              :model: Book
-              :method: type
-              :parameter_type: combobox
-              :parameter_values:
-                - :search_value: book
-                - :search_value: journal
-                - :search_value: article
-                - :search_value: electronic journal
-
-          - :name: "Genre"
-            :unique_identifier: book_genre
-            :search:
-              :model: Book
-              :method: Genre
-              :parameter_type: combobox
-              :parameter_value_categories:
-                - :name: Adventure
-                  :unique_identifier: adventure
-                  :collapse: true
-                  :display_order: 1
-                - :name: Comic novel
-                  :unique_identifier: comic
-                - :name: Historical
-                  :unique_identifier: historical
-              :parameter_values:
-                - :search_value: "Robinsonade"
-                  :parameter_value_category: adventure
-                - :search_value: "Black comedy"
-                  :parameter_value_category: comic
-                - :search_value: "Parody"
-                  :parameter_value_category: comic
-                - :search_value: "Lost World"
-                  :parameter_value_category: adventure
-                - :search_value: "Brit lit"
-                - :search_value: "Pulp fiction"
-
-          - :name: "Title"
-            :unique_identifier: title
-            :search:
-              :model: Book
-              :method: title
-              :parameter_type: text
-
-          - :name: "Keyword"
-            :unique_identifier: text
-            :search:
-              :model: Book
-              :method: text
-              :parameter_type: text
-