abstractor 4.2.2 → 4.2.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/views/abstractor/abstractor_abstractions/_ungrouped_abstractions_list.html.haml

@@ -1,5 +1,5 @@
 .abstractor_abstractions_ungrouped
-  - ungrouped_subjects = about.class.abstractor_subjects(grouped: false, namespace_type: namespace_type, namespace_id: namespace_id)
+  - ungrouped_subjects = about.class.abstractor_subjects(grouped: false, namespace_type: namespace_type, namespace_id: namespace_id).order('abstractor_subjects.id')
   - if ungrouped_subjects.any?
     %fieldset
       .abstractor_abstractions_header

data/app/views/abstractor/abstractor_abstractions/edit.html.haml

@@ -9,6 +9,8 @@
       - case abstraction_schema.abstractor_object_type.value
       - when 'date'
         = f.text_field :value, class: 'abstractor_datepicker'
+      - when 'text'
+        = f.text_area :value
       - when 'string'
         = f.text_field :value
       - when 'number'

data/db/migrate/20150223033848_add_custom_nlp_provider_to_abstractor_abstraction_sources.rb

@@ -0,0 +1,5 @@
+class AddCustomNlpProviderToAbstractorAbstractionSources < ActiveRecord::Migration
+  def change
+    add_column :abstractor_abstraction_sources, :custom_nlp_provider, :string
+  end
+end

data/lib/abstractor/custom_nlp_provider.rb

@@ -0,0 +1,112 @@
+module Abstractor
+  module CustomNlpProvider
+    ##
+    # Determines the suggestion endpoint for the passed in custom NLP provider.
+    #
+    # The endpoint is assumed to be configured in config/abstractor/custom_nlp_providers.yml.
+    # A template configratuon file can be generated in the host application by
+    # calling the rake task abstractor:custom_nlp_provider.
+    # @param [String] custom_nlp_provider The name of the custom NLP provider whose endpoint should be determined.
+    # @return [String] The endpoint.
+    def self.determine_suggestion_endpoint(custom_nlp_provider)
+      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_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::AbstractorAbstraction] abstractor_abstraction The abstractor abstraction to be formated for submission to a custom nlp provider endpoint.
+    # @param [Abstractor::AbstractorAbstractionSource] abstractor_abstraction_source The abstractor abstraction source to be formated for submission to a custom nlp provider endpoint.
+    # @param [String] abstractor_text The text be formated for submission to a custom nlp provider endpoint.
+    # @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_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
+      }
+    end
+  end
+end

data/lib/abstractor/enum.rb

@@ -10,5 +10,10 @@ module Abstractor
 
     ABSTRACTOR_SECTION_TYPE_CUSTOM = 'custom'
     ABSTRACTOR_SECTION_TYPE_NAME_VALUE = 'name/value'
+
+    ABSTRACTOR_SUGGESTION_STATUS_NEEDS_REVIEW = 'Needs review'
+    ABSTRACTOR_SUGGESTION_STATUS_ACCEPTED = 'Accepted'
+    ABSTRACTOR_SUGGESTION_STATUS_REJECTED = 'Rejected'
+    ABSTRACTOR_SUGGESTION_STATUSES = [ABSTRACTOR_SUGGESTION_STATUS_NEEDS_REVIEW, ABSTRACTOR_SUGGESTION_STATUS_ACCEPTED, ABSTRACTOR_SUGGESTION_STATUS_REJECTED]
   end
 end

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

@@ -4,6 +4,25 @@ module Abstractor
       module AbstractorSuggestionsController
         def self.included(base)
           base.send :before_filter, :set_abstractor_suggestion, :only => [:update]
+          base.send :before_filter, :set_abstractor_abstraction
+        end
+
+        def create
+          respond_to do |format|
+            begin
+              suggestion = params[:abstractor_suggestion]
+              abstractor_abstraction_source = Abstractor::AbstractorAbstractionSource.find(suggestion[:abstractor_abstraction_source_id])
+              abstractor_suggestion = nil
+              Abstractor::AbstractorSuggestion.transaction do
+                suggestion[:suggestion_sources].each do |suggestion_source|
+                  abstractor_suggestion = @abstractor_abstraction.abstractor_subject.suggest(@abstractor_abstraction, abstractor_abstraction_source, suggestion_source[:match_value], suggestion_source[:sentence_match_value], suggestion[:source_id], suggestion[:source_type], suggestion[:source_method], nil, suggestion[:value], suggestion[:unknown], suggestion[:not_applicable], nil, nil)
+                end
+              end
+              format.json { render json: abstractor_suggestion, status: :created }
+            rescue => e
+              format.json { render json: "Error processing request to create abstractor suggestions: #{e}", status: :unprocessable_entity }
+            end
+          end
         end
 
         def update
@@ -17,12 +36,15 @@ module Abstractor
         end
 
         private
-          def set_abstractor_suggestion
+          def set_abstractor_abstraction
             @abstractor_abstraction = Abstractor::AbstractorAbstraction.find(params[:abstractor_abstraction_id])
-            @abstractor_suggestion = Abstractor::AbstractorSuggestion.find(params[:id])
             @about = @abstractor_abstraction.about
           end
 
+          def set_abstractor_suggestion
+            @abstractor_suggestion = Abstractor::AbstractorSuggestion.find(params[:id])
+          end
+
           def abstractor_suggestion_params
             params.require(:abstractor_suggestion).permit(:id, :abstractor_abstraction_id, :abstractor_suggestion_status_id, :suggested_value, :unknown, :not_applicable, :deleted_at, :_destroy)
           end

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

@@ -90,6 +90,28 @@ module Abstractor
               ais.abstractor_abstraction_source == abstractor_abstraction_source
             end
           end
+
+          ##
+          # Returns all the suggestions for the abstraction with a suggestion status of 'needs review'
+          #
+          # @return [ActiveRecord::Relation] List of [Abstractor::AbstractorSuggestion].
+          def unreviewed_abstractor_suggestions
+            abstractor_suggestions.select { |abstractor_suggestion| abstractor_suggestion.abstractor_suggestion_status.name == Abstractor::Enum::ABSTRACTOR_SUGGESTION_STATUS_NEEDS_REVIEW }
+          end
+
+          ##
+          # Remove suggestions on the abstraction with a suggestion status of 'needs review' that are not present in the array of hashes representing suggestions passed in.
+          #
+          # @param [Array<Hash>] suggestions
+          # @return [void]
+          def remove_unreviewed_suggestions_not_matching_suggestions(suggestions)
+            unreviewed_abstractor_suggestions.each do |abstractor_suggestion|
+              not_detritus = suggestions.detect { |suggestion| suggestion[:suggestion] == abstractor_suggestion.suggested_value }
+              unless not_detritus
+                abstractor_suggestion.destroy
+              end
+            end
+          end
         end
 
         module ClassMethods

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

@@ -1,3 +1,4 @@
+require 'rest_client'
 module Abstractor
   module Methods
     module Models
@@ -37,6 +38,7 @@ module Abstractor
           # * 'nlp suggestion': creates instances of Abstractor::AbstractorSuggestion based on natural language processing (nlp) logic searching the text provided by the Abstractor::AbstractorSubject#from_methd attribute.
           # * 'custom suggestion': creates instances of Abstractor::AbstractorSuggestion based on custom logic delegated to the method configured in AbstractorAbstractionSource#custom_method.
           # * 'indirect': creates an instance of Abstractor::AbstractorIndirectSource wih null source_type, source_id, source_method attributes -- all waiting to be set upon selection of an indirect source.
+          # * 'custom nlp suggestion': 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.
           #
           # @param [ActiveRecord::Base] about The entity to abstract.  An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.
           # @return [void]
@@ -51,6 +53,8 @@ module Abstractor
                 abstract_custom_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
               when 'indirect'
                 abstract_indirect_source(about, abstractor_abstraction, abstractor_abstraction_source)
+              when 'custom nlp suggestion'
+                abstract_custom_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
               end
             end
           end
@@ -127,13 +131,66 @@ module Abstractor
           # @param [Abstractor::AbstractorAbstractionSource] abstractor_abstraction_source The instance of the Abstractor::AbstractorAbstractionSource that provides the custom method to invoke on the abstractable entity to make custom suggestions.
           # @return [void]
           def abstract_custom_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
-            suggestions = about.send(abstractor_abstraction_source.custom_method)
+            suggestions = about.send(abstractor_abstraction_source.custom_method, abstractor_abstraction)
             suggestions.each do |suggestion|
               suggest(abstractor_abstraction, abstractor_abstraction_source, nil, nil, about.id, about.class.to_s, abstractor_abstraction_source.from_method, abstractor_abstraction_source.section_name, suggestion[:suggestion], nil, nil, abstractor_abstraction_source.custom_method, suggestion[:explanation])
             end
             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.
+          #
+          # The method will determine an endpoint by looking in
+          # config/abstractor/custom_nlp_providers.yml based on the current environment
+          # and the value of the AbstractorAbstractionSource#custom_nlp_provider attribute.
+          #
+          # A template configratuon file can be generated in the the host application by
+          # calling the rake task abstractor:custom_nlp_provider.  The configuration
+          # is expected to provide different endpoints per environment, per provider.
+          # Abstractor will format a JSON body to post to the discovered endpoint.
+          # The custom NLP provider will be expected to generate suggestions
+          # and post them back to /abstractor_abstractions/:abstractor_abstraction_id/abstractor_suggestions/
+          # @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 [ActiveRecord::Base] about The entity to abstract.  An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.
+          # @param [Abstractor::AbstractorAbstraction] abstractor_abstraction The instance of Abstractor::AbstractorAbstraction to make suggestions against.
+          # @param [Abstractor::AbstractorAbstractionSource] abstractor_abstraction_source The instance of the Abstractor::AbstractorAbstractionSource that provides the name of the custom NLP provider.
+          # @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)
+              RestClient.post(suggestion_endpoint, body.to_json, content_type: :json)
+            end
+          end
+
           def abstract_unknown(about, abstractor_abstraction, abstractor_abstraction_source)
             create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
           end

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

@@ -9,10 +9,10 @@ module Abstractor
           base.send :belongs_to, :abstractor_abstraction
           base.send :belongs_to, :abstractor_suggestion_status
 
-          base.send :has_one, :abstractor_suggestion_object_value
-          base.send :has_one, :abstractor_object_value, :through => :abstractor_suggestion_object_value
+          base.send :has_one, :abstractor_suggestion_object_value, dependent: :destroy
+          base.send :has_one, :abstractor_object_value, through: :abstractor_suggestion_object_value
 
-          base.send :has_many, :abstractor_suggestion_sources
+          base.send :has_many, :abstractor_suggestion_sources, dependent: :destroy
 
           # base.send :attr_accessible, :abstractor_abstraction, :abstractor_abstraction_id, :abstractor_suggestion_sources, :abstractor_suggestion_source_id, :abstractor_suggestion_status, :abstractor_suggestion_status_id, :suggested_value, :deleted_at, :unknown, :not_applicable
 

data/lib/abstractor/setup.rb

@@ -9,6 +9,7 @@ module Abstractor
       Abstractor::AbstractorObjectType.where(value: 'radio button list').first_or_create
       Abstractor::AbstractorObjectType.where(value: 'date').first_or_create
       Abstractor::AbstractorObjectType.where(value: 'dynamic list').first_or_create
+      Abstractor::AbstractorObjectType.where(value: 'text').first_or_create
 
       puts 'Setting up Abstractor::AbstractorRuleType'
       Abstractor::AbstractorRuleType.where(name: 'name/value', description:'search for value associated with name').first_or_create
@@ -28,6 +29,7 @@ module Abstractor
       Abstractor::AbstractorAbstractionSourceType.where(name: 'nlp suggestion').first_or_create
       Abstractor::AbstractorAbstractionSourceType.where(name: 'custom suggestion').first_or_create
       Abstractor::AbstractorAbstractionSourceType.where(name: 'indirect').first_or_create
+      Abstractor::AbstractorAbstractionSourceType.where(name: 'custom nlp suggestion').first_or_create
 
       puts 'Setting up Abstractor::AbstractorSectionType'
       Abstractor::AbstractorSectionType.where(name: Abstractor::Enum::ABSTRACTOR_SECTION_TYPE_CUSTOM).first_or_create

data/lib/abstractor/version.rb

@@ -1,3 +1,3 @@
 module Abstractor
-  VERSION = '4.2.2'
+  VERSION = '4.2.3'
 end

data/lib/tasks/abstractor_tasks.rake

@@ -1,5 +1,6 @@
 require 'open-uri'
 require 'zip'
+require 'fileutils'
 
 namespace :abstractor do
   namespace :setup do
@@ -26,6 +27,28 @@ namespace :abstractor do
         fo.print open('https://github.com/louismullie/stanford-core-nlp/blob/master/bin/bridge.jar?raw=true').read
       end
     end
+
+    desc "Custom NLP provider"
+    task(custom_nlp_provider: :environment) do
+      FileUtils.mkdir_p 'config/abstractor'
+
+template = <<EOS
+# Add the actual name of your custom nlp provider.
+# Specify the sugestion endpoint per environemnt.
+custom_nlp_provider_name:
+  suggestion_endpoint:
+      development: http://custom-nlp-provider.dev/suggest
+      test: http://custom-nlp-provider.test/suggest
+      staging: http://custom-nlp-provider-staging.org/suggest
+      production: http://custom-nlp-provider.org/suggest
+EOS
+
+      if !File.exist?('config/abstractor/custom_nlp_providers.yml')
+        File.open('config/abstractor/custom_nlp_providers.yml', 'w+'){ |f|
+          f << template
+        }
+      end
+    end
   end
 
   private

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: abstractor
 version: !ruby/object:Gem::Version
-  version: 4.2.2
+  version: 4.2.3
 platform: ruby
 authors:
 - Michael Gurley, Yulia Bushmanova
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-21 00:00:00.000000000 Z
+date: 2015-03-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -119,25 +119,25 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 3.0.0
 - !ruby/object:Gem::Dependency
-  name: stanford-core-nlp
+  name: stanford-core-nlp-abstractor
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.5.1
+        version: 0.5.3
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.5.1
+        version: 0.5.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.5.1
+        version: 0.5.3
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.5.1
+        version: 0.5.3
 - !ruby/object:Gem::Dependency
   name: rubyzip
   requirement: !ruby/object:Gem::Requirement
@@ -178,6 +178,26 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.7.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.7.0
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
@@ -398,6 +418,26 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 3.1.1
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.0
 description: A Rails engine gem for deriving discrete data points from narrative text
   via natural language processing (NLP).  The gem includes a user interface to present
   the abstracted data points for confirmation/revision by curator.
@@ -513,10 +553,12 @@ files:
 - db/migrate/20141107171413_add_sectioning.rb
 - 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/seeds.rb
 - lib/abstractor.rb
 - lib/abstractor/abstractable.rb
 - lib/abstractor/core_ext/string.rb
+- lib/abstractor/custom_nlp_provider.rb
 - lib/abstractor/engine.rb
 - lib/abstractor/enum.rb
 - lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb