abstractor 4.2.3 → 4.3.0
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- checksums.yaml +4 -4
- data/app/controllers/abstractor/abstractor_abstraction_schemas_controller.rb +5 -0
- data/config/routes.rb +3 -0
- data/db/migrate/20150317172523_add_properties_to_abstractor_object_values.rb +5 -0
- data/db/migrate/20150317204748_add_vocabulary_columns_to_abstractor_object_values.rb +7 -0
- data/lib/abstractor/custom_nlp_provider.rb +4 -68
- data/lib/abstractor/methods/controllers/abstractor_abstraction_schemas_controller.rb +23 -0
- data/lib/abstractor/methods/models/abstractor_subject.rb +4 -20
- data/lib/abstractor/serializers/abstractor_abstraction_schema_serializer.rb +34 -0
- data/lib/abstractor/version.rb +1 -1
- data/lib/generators/abstractor/install/install_generator.rb +1 -0
- data/lib/tasks/abstractor_tasks.rake +17 -0
- metadata +7 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e12e1a6577e6efe1216cce735b4bf8430bb6d2c6
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4
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data.tar.gz: d92a5873f58d49d1bb637b604d5a9e387b437b7f
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9dbc5beb80be2775fa9776557fc565d6fed3480a891c893c4252df7297facff07f5c17c46a15f03d9fecb0c1ec2fc97b6e417938bc1a9c9ccfec4e4ee6708705
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7
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data.tar.gz: 764ae53872aafc7c7aac5628609d8f208a60f2cb24ac3468d90903555e74b6fac565120f1d0721e2e28454d7ef50bce4d12ea40a8a5b4780d923ed249411db11
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data/config/routes.rb
CHANGED
@@ -0,0 +1,7 @@
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+
class AddVocabularyColumnsToAbstractorObjectValues < ActiveRecord::Migration
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def change
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add_column :abstractor_object_values, :vocabulary_code, :string
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add_column :abstractor_object_values, :vocabulary, :string
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add_column :abstractor_object_values, :vocabulary_version, :string
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end
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end
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@@ -12,81 +12,18 @@ module Abstractor
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suggestion_endpoint = YAML.load_file("#{Rails.root}/config/abstractor/custom_nlp_providers.yml")[custom_nlp_provider]['suggestion_endpoint'][Rails.env]
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end
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##
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# Formats the object values and object value variants for the passed in Abstractor::AbstractorSubject.
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#
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# Preperation for submision to a custom NLP provider endpoint.
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#
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# @example Example of body prepared by Abstractor to submit to an custom NLP provider
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# {
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# "abstractor_abstraction_schema_id":1,
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# "abstractor_abstraction_id":1,
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# "abstractor_abstraction_source_id":1,
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# "source_type": "PathologyCase",
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# "source_method": "note_text",
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# "text": "The patient has a diagnosis of glioblastoma. GBM does not have a good prognosis. But I can't rule out meningioma.",
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# "object_values": [
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# { "value": "glioblastoma, nos",
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# "object_value_variants":[
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# { "value": "glioblastoma" },
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# { "value": "gbm" },
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# { "value": "spongioblastoma multiforme"}
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# ]
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# },
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# { "value": "meningioma, nos",
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# "object_value_variants":[
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# { "value": "meningioma" },
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# { "value": "leptomeningioma" },
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# { "value": "meningeal fibroblastoma" }
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# ]
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# }
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# ]
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# }
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#
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#
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# @param [Abstractor::AbstractorSubject] abstractor_subject The abstractor subject having the desired object values.
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# @return [Hash]
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-
def self.abstractor_object_values(abstractor_subject)
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object_values = []
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abstractor_subject.abstractor_abstraction_schema.abstractor_object_values.each do |abstractor_object_value|
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object_value = {}
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object_value[:value] = abstractor_object_value.value
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object_value[:object_value_variants] = []
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abstractor_object_value.abstractor_object_value_variants.each do |abstractor_object_value_variant|
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-
object_value[:object_value_variants] << { value: abstractor_object_value_variant.value }
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-
end
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object_values << object_value
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-
end
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object_values
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-
end
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-
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##
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# Formats the JSON body in preparation for submision to a custom NLP provider endpoint.
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#
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# @example Example of body prepared by Abstractor to submit to an custom NLP provider
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# {
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# "abstractor_abstraction_schema_id":1,
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# "abstractor_abstraction_schema_uri":"https://moomin.com/abstractor_abstraction_schemas/1",
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# "abstractor_abstraction_id":1,
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# "abstractor_abstraction_source_id":1,
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# "source_type": "PathologyCase",
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# "source_method": "note_text",
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# "text": "The patient has a diagnosis of glioblastoma. GBM does not have a good prognosis. But I can't rule out meningioma."
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# "object_values": [
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# { "value": "glioblastoma, nos",
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# "object_value_variants":[
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# { "value": "glioblastoma" },
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# { "value": "gbm" },
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# { "value": "spongioblastoma multiforme"}
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# ]
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# },
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# { "value": "meningioma, nos",
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# "object_value_variants":[
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# { "value": "meningioma" },
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# { "value": "leptomeningioma" },
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# { "value": "meningeal fibroblastoma" }
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# ]
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# }
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# ]
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# "text": "The patient has a diagnosis of glioblastoma. GBM does not have a good prognosis. But I can't rule out meningioma."
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# }
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#
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#
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@@ -96,16 +33,15 @@ module Abstractor
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33
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# @param [Hash] source The hash of values representing the source for submission to a custom nlp provider endpoint.
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34
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# @return [Hash] The formatted body.
|
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35
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def self.format_body_for_suggestion_endpoint(abstractor_abstraction, abstractor_abstraction_source, abstractor_text, source)
|
99
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-
object_values = CustomNlpProvider.abstractor_object_values(abstractor_abstraction.abstractor_subject)
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36
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{
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101
37
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abstractor_abstraction_schema_id: abstractor_abstraction.abstractor_subject.abstractor_abstraction_schema.id,
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38
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+
abstractor_abstraction_schema_uri: Abstractor::Engine.routes.url_helpers.abstractor_abstraction_schema_url(abstractor_abstraction.abstractor_subject.abstractor_abstraction_schema),
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102
39
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abstractor_abstraction_id: abstractor_abstraction.id,
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abstractor_abstraction_source_id: abstractor_abstraction_source.id,
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source_id: source[:source_id],
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source_type: source[:source_type].to_s,
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43
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source_method: source[:source_method],
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text: abstractor_text
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object_values: object_values
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text: abstractor_text
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}
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end
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47
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end
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@@ -0,0 +1,23 @@
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module Abstractor
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module Methods
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module Controllers
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module AbstractorAbstractionSchemasController
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5
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def self.included(base)
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6
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base.send :helper, :all
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7
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base.send :before_filter, :set_abstractor_abstraction_schema, only: :show
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end
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9
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def show
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11
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respond_to do |format|
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12
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format.json { render json: Abstractor::Serializers::AbstractorAbstractionSchemaSerializer.new(@abstractor_abstraction_schema).as_json }
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13
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end
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end
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private
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def set_abstractor_abstraction_schema
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18
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@abstractor_abstraction_schema = Abstractor::AbstractorAbstractionSchema.find(params[:id])
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end
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end
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end
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end
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end
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@@ -138,8 +138,8 @@ module Abstractor
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138
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create_unknown_abstractor_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
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139
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end
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140
140
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141
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-
# Looks up a suggestion endpoint to submit text
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-
#
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+
# Looks up a suggestion endpoint to submit text to an external
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+
# custom NLP provider for the delegation of suggestion generation.
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#
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# The method will determine an endpoint by looking in
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# config/abstractor/custom_nlp_providers.yml based on the current environment
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@@ -154,27 +154,12 @@ module Abstractor
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154
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# @example Example of body prepared by Abstractor to submit to an custom NLP provider
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155
155
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# {
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156
156
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# "abstractor_abstraction_schema_id":1,
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+
# "abstractor_abstraction_schema_uri":"https://moomin.com/abstractor_abstraction_schemas/1",
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# "abstractor_abstraction_id":1,
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# "abstractor_abstraction_source_id":1,
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# "source_type": "PathologyCase",
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# "source_method": "note_text",
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-
# "text": "The patient has a diagnosis of glioblastoma. GBM does not have a good prognosis. But I can't rule out meningioma."
|
162
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-
# "object_values": [
|
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# { "value": "glioblastoma, nos",
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# "object_value_variants":[
|
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# { "value": "glioblastoma" },
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# { "value": "gbm" },
|
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# { "value": "spongioblastoma multiforme"}
|
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-
# ]
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# },
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# { "value": "meningioma, nos",
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# "object_value_variants":[
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-
# { "value": "meningioma" },
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# { "value": "leptomeningioma" },
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# { "value": "meningeal fibroblastoma" }
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# ]
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# }
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-
# ]
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+
# "text": "The patient has a diagnosis of glioblastoma. GBM does not have a good prognosis. But I can't rule out meningioma."
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# }
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#
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# @param [ActiveRecord::Base] about The entity to abstract. An instance of the class specified in the Abstractor::AbstractorSubject#subject_type attribute.
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@@ -183,7 +168,6 @@ module Abstractor
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168
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# @return [void]
|
184
169
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def abstract_custom_nlp_suggestion(about, abstractor_abstraction, abstractor_abstraction_source)
|
185
170
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suggestion_endpoint = CustomNlpProvider.determine_suggestion_endpoint(abstractor_abstraction_source.custom_nlp_provider)
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186
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-
object_values = CustomNlpProvider.abstractor_object_values(self)
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171
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abstractor_abstraction_source.normalize_from_method_to_sources(about).each do |source|
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abstractor_text = Abstractor::AbstractorAbstractionSource.abstractor_text(source)
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body = Abstractor::CustomNlpProvider.format_body_for_suggestion_endpoint(abstractor_abstraction, abstractor_abstraction_source, abstractor_text, source)
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@@ -0,0 +1,34 @@
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require 'json'
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2
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module Abstractor
|
3
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module Serializers
|
4
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class AbstractorAbstractionSchemaSerializer
|
5
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+
def initialize(abstractor_abstraction_schema)
|
6
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+
@abstractor_abstraction_schema = abstractor_abstraction_schema
|
7
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+
end
|
8
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+
|
9
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def as_json(options = {})
|
10
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{
|
11
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"predicate" => abstractor_abstraction_schema.predicate,
|
12
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+
"display_name" => abstractor_abstraction_schema.display_name,
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13
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+
"abstractor_object_type" => abstractor_abstraction_schema.abstractor_object_type.value,
|
14
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+
"preferred_name" => abstractor_abstraction_schema.preferred_name,
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15
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+
"predicate_variants" => abstractor_abstraction_schema.abstractor_abstraction_schema_predicate_variants.map { |abstractor_abstraction_schema_predicate_variant| { 'value' => abstractor_abstraction_schema_predicate_variant.value } },
|
16
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+
"object_values" => abstractor_abstraction_schema.abstractor_object_values.map do |abstractor_object_value|
|
17
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+
{
|
18
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+
'value' => abstractor_object_value.value,
|
19
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+
'properties' => abstractor_object_value.properties.nil? ? nil : JSON.parse(abstractor_object_value.properties),
|
20
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+
'vocabulary_code' => abstractor_object_value.vocabulary_code,
|
21
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+
'vocabulary' => abstractor_object_value.vocabulary,
|
22
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+
'vocabulary_version' => abstractor_object_value.vocabulary_version,
|
23
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+
'object_value_variants' => abstractor_object_value.abstractor_object_value_variants.map { |abstractor_object_value_variant| { 'value' => abstractor_object_value_variant.value } }
|
24
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+
}
|
25
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+
end
|
26
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+
}
|
27
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+
end
|
28
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+
|
29
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+
private
|
30
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+
|
31
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+
attr_reader :abstractor_abstraction_schema
|
32
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+
end
|
33
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+
end
|
34
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+
end
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data/lib/abstractor/version.rb
CHANGED
@@ -85,6 +85,7 @@ module Abstractor
|
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85
85
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copy_file "controllers/abstractor_abstraction_groups_controller.rb", "#{path}/abstractor_abstraction_groups_controller.rb"
|
86
86
|
copy_file "controllers/abstractor_abstractions_controller.rb", "#{path}/abstractor_abstractions_controller.rb"
|
87
87
|
copy_file "controllers/abstractor_suggestions_controller.rb", "#{path}/abstractor_suggestions_controller.rb"
|
88
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+
copy_file "controllers/abstractor_abstraction_schemas_controller.rb", "#{path}/abstractor_abstraction_schemas_controller.rb"
|
88
89
|
end
|
89
90
|
|
90
91
|
if options["customize-all"] || options["customize-helpers"]
|
@@ -1,6 +1,11 @@
|
|
1
1
|
require 'open-uri'
|
2
2
|
require 'zip'
|
3
3
|
require 'fileutils'
|
4
|
+
require 'thor'
|
5
|
+
|
6
|
+
class Hammer < Thor
|
7
|
+
include Thor::Actions
|
8
|
+
end
|
4
9
|
|
5
10
|
namespace :abstractor do
|
6
11
|
namespace :setup do
|
@@ -48,6 +53,18 @@ EOS
|
|
48
53
|
f << template
|
49
54
|
}
|
50
55
|
end
|
56
|
+
|
57
|
+
puts "Warning! Warning! Warning!"
|
58
|
+
puts "Setting Abstractor::Engine.routes.default_url_options[:host] in config/environemnts/development.rb"
|
59
|
+
puts "Change it as appropriate."
|
60
|
+
|
61
|
+
hammer = Hammer.new
|
62
|
+
hammer.insert_into_file("#{Rails.root}/config/environments/development.rb", :after => /(::Application.configure do\n|application.configure do\n)/) do
|
63
|
+
"
|
64
|
+
Abstractor::Engine.routes.default_url_options[:host] = 'https://moomin.com'
|
65
|
+
|
66
|
+
"
|
67
|
+
end
|
51
68
|
end
|
52
69
|
end
|
53
70
|
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
|
name: abstractor
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 4.
|
4
|
+
version: 4.3.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Michael Gurley, Yulia Bushmanova
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2015-03-
|
11
|
+
date: 2015-03-18 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rails
|
@@ -480,6 +480,7 @@ files:
|
|
480
480
|
- app/assets/stylesheets/abstractor/application.css.scss
|
481
481
|
- app/assets/stylesheets/abstractor/jquery.ui.override.css.scss
|
482
482
|
- app/controllers/abstractor/abstractor_abstraction_groups_controller.rb
|
483
|
+
- app/controllers/abstractor/abstractor_abstraction_schemas_controller.rb
|
483
484
|
- app/controllers/abstractor/abstractor_abstractions_controller.rb
|
484
485
|
- app/controllers/abstractor/abstractor_suggestions_controller.rb
|
485
486
|
- app/controllers/abstractor/application_controller.rb
|
@@ -554,6 +555,8 @@ files:
|
|
554
555
|
- db/migrate/20141120044606_add_system_generated_to_abstractor_abstraction_groups.rb
|
555
556
|
- db/migrate/20150110002921_create_indexes_for_performance.rb
|
556
557
|
- db/migrate/20150223033848_add_custom_nlp_provider_to_abstractor_abstraction_sources.rb
|
558
|
+
- db/migrate/20150317172523_add_properties_to_abstractor_object_values.rb
|
559
|
+
- db/migrate/20150317204748_add_vocabulary_columns_to_abstractor_object_values.rb
|
557
560
|
- db/seeds.rb
|
558
561
|
- lib/abstractor.rb
|
559
562
|
- lib/abstractor/abstractable.rb
|
@@ -562,6 +565,7 @@ files:
|
|
562
565
|
- lib/abstractor/engine.rb
|
563
566
|
- lib/abstractor/enum.rb
|
564
567
|
- lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb
|
568
|
+
- lib/abstractor/methods/controllers/abstractor_abstraction_schemas_controller.rb
|
565
569
|
- lib/abstractor/methods/controllers/abstractor_abstractions_controller.rb
|
566
570
|
- lib/abstractor/methods/controllers/abstractor_suggestions_controller.rb
|
567
571
|
- lib/abstractor/methods/models/abstractor_abstraction.rb
|
@@ -593,6 +597,7 @@ files:
|
|
593
597
|
- lib/abstractor/methods/models/soft_delete.rb
|
594
598
|
- lib/abstractor/negation_detection.rb
|
595
599
|
- lib/abstractor/parser.rb
|
600
|
+
- lib/abstractor/serializers/abstractor_abstraction_schema_serializer.rb
|
596
601
|
- lib/abstractor/setup.rb
|
597
602
|
- lib/abstractor/user_interface.rb
|
598
603
|
- lib/abstractor/utility.rb
|