abstractor 4.2.3 → 4.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 10fb7cb823fa9ef4b2b0ccddb481d461fe3d6cc1
+  metadata.gz: e12e1a6577e6efe1216cce735b4bf8430bb6d2c6
+  data.tar.gz: d92a5873f58d49d1bb637b604d5a9e387b437b7f
 SHA512:
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+  data.tar.gz: 764ae53872aafc7c7aac5628609d8f208a60f2cb24ac3468d90903555e74b6fac565120f1d0721e2e28454d7ef50bce4d12ea40a8a5b4780d923ed249411db11

data/app/controllers/abstractor/abstractor_abstraction_schemas_controller.rb

@@ -0,0 +1,5 @@
+module Abstractor
+  class AbstractorAbstractionSchemasController < Abstractor::ApplicationController
+    include Abstractor::Methods::Controllers::AbstractorAbstractionSchemasController
+  end
+end

data/config/routes.rb

@@ -7,4 +7,7 @@ Abstractor::Engine.routes.draw do
     end
     resources :abstractor_suggestions
   end
+
+  resources :abstractor_abstraction_schemas do
+  end
 end

data/db/migrate/20150317172523_add_properties_to_abstractor_object_values.rb

@@ -0,0 +1,5 @@
+class AddPropertiesToAbstractorObjectValues < ActiveRecord::Migration
+  def change
+    add_column :abstractor_object_values, :properties, :text
+  end
+end

data/db/migrate/20150317204748_add_vocabulary_columns_to_abstractor_object_values.rb

@@ -0,0 +1,7 @@
+class AddVocabularyColumnsToAbstractorObjectValues < ActiveRecord::Migration
+  def change
+    add_column :abstractor_object_values, :vocabulary_code, :string
+    add_column :abstractor_object_values, :vocabulary, :string
+    add_column :abstractor_object_values, :vocabulary_version, :string
+  end
+end

data/lib/abstractor/custom_nlp_provider.rb

@@ -12,81 +12,18 @@ module Abstractor
       suggestion_endpoint = YAML.load_file("#{Rails.root}/config/abstractor/custom_nlp_providers.yml")[custom_nlp_provider]['suggestion_endpoint'][Rails.env]
     end
 
-    ##
-    # Formats the object values and object value variants for the passed in Abstractor::AbstractorSubject.
-    #
-    # Preperation for submision to a custom NLP provider endpoint.
-    #
-    # @example Example of body prepared by Abstractor to submit to an custom NLP provider
-    #   {
-    #     "abstractor_abstraction_schema_id":1,
-    #     "abstractor_abstraction_id":1,
-    #     "abstractor_abstraction_source_id":1,
-    #     "source_type":  "PathologyCase",
-    #     "source_method": "note_text",
-    #     "text": "The patient has a diagnosis of glioblastoma.  GBM does not have a good prognosis.  But I can't rule out meningioma.",
-    #     "object_values": [
-    #       { "value": "glioblastoma, nos",
-    #         "object_value_variants":[
-    #           { "value": "glioblastoma" },
-    #           { "value": "gbm" },
-    #           { "value": "spongioblastoma multiforme"}
-    #         ]
-    #       },
-    #       { "value": "meningioma, nos",
-    #         "object_value_variants":[
-    #           { "value": "meningioma" },
-    #           { "value": "leptomeningioma" },
-    #           { "value": "meningeal fibroblastoma" }
-    #         ]
-    #       }
-    #     ]
-    #   }
-    #
-    #
-    # @param [Abstractor::AbstractorSubject] abstractor_subject The abstractor subject having the desired object values.
-    # @return [Hash]
-    def self.abstractor_object_values(abstractor_subject)
-      object_values = []
-      abstractor_subject.abstractor_abstraction_schema.abstractor_object_values.each do |abstractor_object_value|
-        object_value = {}
-        object_value[:value] = abstractor_object_value.value
-        object_value[:object_value_variants] = []
-        abstractor_object_value.abstractor_object_value_variants.each do |abstractor_object_value_variant|
-          object_value[:object_value_variants] << { value: abstractor_object_value_variant.value }
-        end
-        object_values << object_value
-      end
-      object_values
-    end
-
     ##
     # Formats the JSON body in preparation for submision to a custom NLP provider endpoint.
     #
     # @example Example of body prepared by Abstractor to submit to an custom NLP provider
     #   {
     #     "abstractor_abstraction_schema_id":1,
+    #     "abstractor_abstraction_schema_uri":"https://moomin.com/abstractor_abstraction_schemas/1",
     #     "abstractor_abstraction_id":1,
     #     "abstractor_abstraction_source_id":1,
     #     "source_type":  "PathologyCase",
     #     "source_method": "note_text",
-    #     "text": "The patient has a diagnosis of glioblastoma.  GBM does not have a good prognosis.  But I can't rule out meningioma.",
-    #     "object_values": [
-    #       { "value": "glioblastoma, nos",
-    #         "object_value_variants":[
-    #           { "value": "glioblastoma" },
-    #           { "value": "gbm" },
-    #           { "value": "spongioblastoma multiforme"}
-    #         ]
-    #       },
-    #       { "value": "meningioma, nos",
-    #         "object_value_variants":[
-    #           { "value": "meningioma" },
-    #           { "value": "leptomeningioma" },
-    #           { "value": "meningeal fibroblastoma" }
-    #         ]
-    #       }
-    #     ]
+    #     "text": "The patient has a diagnosis of glioblastoma.  GBM does not have a good prognosis.  But I can't rule out meningioma."
     #   }
     #
     #
@@ -96,16 +33,15 @@ module Abstractor
     # @param [Hash] source The hash of values representing the source for submission to a custom nlp provider endpoint.
     # @return [Hash] The formatted body.
     def self.format_body_for_suggestion_endpoint(abstractor_abstraction, abstractor_abstraction_source, abstractor_text, source)
-      object_values = CustomNlpProvider.abstractor_object_values(abstractor_abstraction.abstractor_subject)
       {
         abstractor_abstraction_schema_id: abstractor_abstraction.abstractor_subject.abstractor_abstraction_schema.id,
+        abstractor_abstraction_schema_uri: Abstractor::Engine.routes.url_helpers.abstractor_abstraction_schema_url(abstractor_abstraction.abstractor_subject.abstractor_abstraction_schema),
         abstractor_abstraction_id: abstractor_abstraction.id,
         abstractor_abstraction_source_id: abstractor_abstraction_source.id,
         source_id: source[:source_id],
         source_type: source[:source_type].to_s,
         source_method: source[:source_method],
-        text: abstractor_text,
-        object_values: object_values
+        text: abstractor_text
       }
     end
   end

data/lib/abstractor/methods/controllers/abstractor_abstraction_schemas_controller.rb

@@ -0,0 +1,23 @@
+module Abstractor
+  module Methods
+    module Controllers
+      module AbstractorAbstractionSchemasController
+        def self.included(base)
+          base.send :helper, :all
+          base.send :before_filter, :set_abstractor_abstraction_schema, only: :show
+        end
+
+        def show
+          respond_to do |format|
+            format.json { render json: Abstractor::Serializers::AbstractorAbstractionSchemaSerializer.new(@abstractor_abstraction_schema).as_json }
+          end
+        end
+
+        private
+          def set_abstractor_abstraction_schema
+            @abstractor_abstraction_schema = Abstractor::AbstractorAbstractionSchema.find(params[:id])
+          end
+      end
+    end
+  end
+end

data/lib/abstractor/methods/models/abstractor_subject.rb

@@ -138,8 +138,8 @@ module Abstractor
             create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
           end
 
-          # Looks up a suggestion endpoint to submit text, object values and object value variants
-          # to an external, custom NLP provider for the delegation of suggestion generation.
+          # Looks up a suggestion endpoint to submit text to an external
+          # custom NLP provider for the delegation of suggestion generation.
           #
           # The method will determine an endpoint by looking in
           # config/abstractor/custom_nlp_providers.yml based on the current environment
@@ -154,27 +154,12 @@ module Abstractor
           # @example Example of body prepared by Abstractor to submit to an custom NLP provider
           #   {
           #     "abstractor_abstraction_schema_id":1,
+          #     "abstractor_abstraction_schema_uri":"https://moomin.com/abstractor_abstraction_schemas/1",
           #     "abstractor_abstraction_id":1,
           #     "abstractor_abstraction_source_id":1,
           #     "source_type":  "PathologyCase",
           #     "source_method": "note_text",
-          #     "text": "The patient has a diagnosis of glioblastoma.  GBM does not have a good prognosis.  But I can't rule out meningioma.",
-          #     "object_values": [
-          #       { "value": "glioblastoma, nos",
-          #         "object_value_variants":[
-          #           { "value": "glioblastoma" },
-          #           { "value": "gbm" },
-          #           { "value": "spongioblastoma multiforme"}
-          #         ]
-          #       },
-          #       { "value": "meningioma, nos",
-          #         "object_value_variants":[
-          #           { "value": "meningioma" },
-          #           { "value": "leptomeningioma" },
-          #           { "value": "meningeal fibroblastoma" }
-          #         ]
-          #       }
-          #     ]
+          #     "text": "The patient has a diagnosis of glioblastoma.  GBM does not have a good prognosis.  But I can't rule out meningioma."
           #   }
           #
           # @param [ActiveRecord::Base] about The entity to abstract.  An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.
@@ -183,7 +168,6 @@ module Abstractor
           # @return [void]
           def abstract_custom_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
             suggestion_endpoint = CustomNlpProvider.determine_suggestion_endpoint(abstractor_abstraction_source.custom_nlp_provider)
-            object_values = CustomNlpProvider.abstractor_object_values(self)
             abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
               abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
               body = Abstractor::CustomNlpProvider.format_body_for_suggestion_endpoint(abstractor_abstraction, abstractor_abstraction_source, abstractor_text, source)

data/lib/abstractor/serializers/abstractor_abstraction_schema_serializer.rb

@@ -0,0 +1,34 @@
+require 'json'
+module Abstractor
+  module Serializers
+    class AbstractorAbstractionSchemaSerializer
+      def initialize(abstractor_abstraction_schema)
+        @abstractor_abstraction_schema = abstractor_abstraction_schema
+      end
+
+      def as_json(options = {})
+        {
+          "predicate" => abstractor_abstraction_schema.predicate,
+          "display_name" => abstractor_abstraction_schema.display_name,
+          "abstractor_object_type" => abstractor_abstraction_schema.abstractor_object_type.value,
+          "preferred_name" => abstractor_abstraction_schema.preferred_name,
+          "predicate_variants" => abstractor_abstraction_schema.abstractor_abstraction_schema_predicate_variants.map { |abstractor_abstraction_schema_predicate_variant|  { 'value' => abstractor_abstraction_schema_predicate_variant.value  } },
+          "object_values" => abstractor_abstraction_schema.abstractor_object_values.map do |abstractor_object_value|
+            {
+              'value' => abstractor_object_value.value,
+              'properties' => abstractor_object_value.properties.nil? ? nil : JSON.parse(abstractor_object_value.properties),
+              'vocabulary_code' => abstractor_object_value.vocabulary_code,
+              'vocabulary' => abstractor_object_value.vocabulary,
+              'vocabulary_version' => abstractor_object_value.vocabulary_version,
+              'object_value_variants' => abstractor_object_value.abstractor_object_value_variants.map { |abstractor_object_value_variant| { 'value' => abstractor_object_value_variant.value } }
+            }
+          end
+        }
+      end
+
+      private
+
+        attr_reader :abstractor_abstraction_schema
+    end
+  end
+end

data/lib/abstractor/version.rb

@@ -1,3 +1,3 @@
 module Abstractor
-  VERSION = '4.2.3'
+  VERSION = '4.3.0'
 end

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

@@ -85,6 +85,7 @@ module Abstractor
         copy_file "controllers/abstractor_abstraction_groups_controller.rb", "#{path}/abstractor_abstraction_groups_controller.rb"
         copy_file "controllers/abstractor_abstractions_controller.rb", "#{path}/abstractor_abstractions_controller.rb"
         copy_file "controllers/abstractor_suggestions_controller.rb", "#{path}/abstractor_suggestions_controller.rb"
+        copy_file "controllers/abstractor_abstraction_schemas_controller.rb", "#{path}/abstractor_abstraction_schemas_controller.rb"
       end
 
       if options["customize-all"] || options["customize-helpers"]

data/lib/tasks/abstractor_tasks.rake

@@ -1,6 +1,11 @@
 require 'open-uri'
 require 'zip'
 require 'fileutils'
+require 'thor'
+
+class Hammer < Thor
+  include Thor::Actions
+end
 
 namespace :abstractor do
   namespace :setup do
@@ -48,6 +53,18 @@ EOS
           f << template
         }
       end
+
+      puts "Warning! Warning! Warning!"
+      puts "Setting Abstractor::Engine.routes.default_url_options[:host] in config/environemnts/development.rb"
+      puts "Change it as appropriate."
+
+      hammer = Hammer.new
+      hammer.insert_into_file("#{Rails.root}/config/environments/development.rb", :after => /(::Application.configure do\n|application.configure do\n)/) do
+"
+  Abstractor::Engine.routes.default_url_options[:host] = 'https://moomin.com'
+
+"
+      end
     end
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: abstractor
 version: !ruby/object:Gem::Version
-  version: 4.2.3
+  version: 4.3.0
 platform: ruby
 authors:
 - Michael Gurley, Yulia Bushmanova
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-03 00:00:00.000000000 Z
+date: 2015-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -480,6 +480,7 @@ files:
 - app/assets/stylesheets/abstractor/application.css.scss
 - app/assets/stylesheets/abstractor/jquery.ui.override.css.scss
 - app/controllers/abstractor/abstractor_abstraction_groups_controller.rb
+- app/controllers/abstractor/abstractor_abstraction_schemas_controller.rb
 - app/controllers/abstractor/abstractor_abstractions_controller.rb
 - app/controllers/abstractor/abstractor_suggestions_controller.rb
 - app/controllers/abstractor/application_controller.rb
@@ -554,6 +555,8 @@ files:
 - db/migrate/20141120044606_add_system_generated_to_abstractor_abstraction_groups.rb
 - db/migrate/20150110002921_create_indexes_for_performance.rb
 - db/migrate/20150223033848_add_custom_nlp_provider_to_abstractor_abstraction_sources.rb
+- db/migrate/20150317172523_add_properties_to_abstractor_object_values.rb
+- db/migrate/20150317204748_add_vocabulary_columns_to_abstractor_object_values.rb
 - db/seeds.rb
 - lib/abstractor.rb
 - lib/abstractor/abstractable.rb
@@ -562,6 +565,7 @@ files:
 - lib/abstractor/engine.rb
 - lib/abstractor/enum.rb
 - lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb
+- lib/abstractor/methods/controllers/abstractor_abstraction_schemas_controller.rb
 - lib/abstractor/methods/controllers/abstractor_abstractions_controller.rb
 - lib/abstractor/methods/controllers/abstractor_suggestions_controller.rb
 - lib/abstractor/methods/models/abstractor_abstraction.rb
@@ -593,6 +597,7 @@ files:
 - lib/abstractor/methods/models/soft_delete.rb
 - lib/abstractor/negation_detection.rb
 - lib/abstractor/parser.rb
+- lib/abstractor/serializers/abstractor_abstraction_schema_serializer.rb
 - lib/abstractor/setup.rb
 - lib/abstractor/user_interface.rb
 - lib/abstractor/utility.rb