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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,53 @@ | ||
| module Inferno | ||
| module DSL | ||
| module FHIREvaluation | ||
| class Config | ||
| DEFAULT_FILE = File.join(__dir__, 'config', 'default.yml') | ||
| attr_accessor :data | ||
| class Config | ||
| DEFAULT_FILE = File.join(__dir__, 'config', 'default.yml') | ||
| attr_accessor :data | ||
|
|
||
| # To-do: add config_file as arguments | ||
| def initialize(config_file = nil) | ||
| @data = if config_file.nil? | ||
| YAML.load_file(File.absolute_path(DEFAULT_FILE)) | ||
| else | ||
| YAML.load_file(File.absolute_path(config_file)) | ||
| end | ||
| # To-do: add config_file as arguments | ||
| def initialize(config_file = nil) | ||
| @data = if config_file.nil? | ||
| YAML.load_file(File.absolute_path(DEFAULT_FILE)) | ||
| else | ||
| YAML.load_file(File.absolute_path(config_file)) | ||
| end | ||
|
|
||
| raise(TypeError, 'Malformed configuration') unless @data.is_a?(Hash) | ||
| raise(TypeError, 'Malformed configuration') unless @data.is_a?(Hash) | ||
|
|
||
| def method_missing(name, *args, &) | ||
| section = @data[name.to_s] | ||
| if section | ||
| Section.new(section) | ||
| else | ||
| super | ||
| def method_missing(name, *args, &) | ||
| section = @data[name.to_s] | ||
| if section | ||
| Section.new(section) | ||
| else | ||
| super | ||
| end | ||
| end | ||
|
|
||
| def respond_to_missing?(name, include_private = false) | ||
| @data.key?(name.to_s) || super | ||
| end | ||
| end | ||
| end | ||
|
|
||
| def respond_to_missing?(name, include_private = false) | ||
| @data.key?(name.to_s) || super | ||
| end | ||
| end | ||
| class Section | ||
| def initialize(details) | ||
| @details = details | ||
| end | ||
|
|
||
| class Section | ||
| def initialize(details) | ||
| @details = details | ||
| end | ||
| def method_missing(name, *_args) | ||
| attribute = @details[name.to_s] | ||
| if attribute.is_a?(Hash) | ||
| Section.new(attribute) | ||
| else | ||
| attribute | ||
| end | ||
| end | ||
|
|
||
| def method_missing(name, *_args) | ||
| attribute = @details[name.to_s] | ||
| if attribute.is_a?(Hash) | ||
| Section.new(attribute) | ||
| else | ||
| attribute | ||
| def respond_to_missing?(name, include_private = false) | ||
| @details.key?(name.to_s) || super | ||
| end | ||
| end | ||
| end | ||
|
|
||
| def respond_to_missing?(name, include_private = false) | ||
| @details.key?(name.to_s) || super | ||
| end | ||
| end | ||
| end | ||
| end | ||
| end | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,100 +1,95 @@ | ||
| module FhirEvaluator | ||
| # DataSummary represents the results of performing data characterization. | ||
| # At this point DataSummary isn't actually used by the evaluator. | ||
| # We will bring back when we need it. | ||
|
|
||
| # class DataSummary | ||
| # attr_accessor :root_resource_ids, # All Example (root resource) Ids | ||
| # :root_bundle_resource_ids, # All Example (root resource) Ids that are Bundle | ||
| # :domain_resource_ids, # Domain resource Ids from root and child resources (exclude Bundle) | ||
| # :resource_profile_map, # Resources and corresponding profiles | ||
| # :resource_patient_map, # Resources and corresponding Patient Ids as subject | ||
| # :resource_subject_map # Resources and corresponding subject | ||
| class DataSummary | ||
| attr_accessor :root_resource_ids, # All Example (root resource) Ids | ||
| :root_bundle_resource_ids, # All Example (root resource) Ids that are Bundle | ||
| :domain_resource_ids, # Domain resource Ids from root and child resources (exclude Bundle) | ||
| :resource_profile_map, # Resources and corresponding profiles | ||
| :resource_patient_map, # Resources and corresponding Patient Ids as subject | ||
| :resource_subject_map # Resources and corresponding subject | ||
|
|
||
| # def initialize(data) | ||
| # @root_resource_ids = [] | ||
| # @root_bundle_resource_ids = [] | ||
| # @domain_resource_ids = [] | ||
| # @resource_profile_map = [] | ||
| # @resource_patient_map = [] | ||
| # @resource_subject_map = [] | ||
| def initialize(_data) | ||
| @root_resource_ids = [] | ||
| @root_bundle_resource_ids = [] | ||
| @domain_resource_ids = [] | ||
| @resource_profile_map = [] | ||
| @resource_patient_map = [] | ||
| @resource_subject_map = [] | ||
| end | ||
|
|
||
| # validate(data) | ||
| # summarize(data) | ||
| # end | ||
| def validate(data) | ||
| resource_ids = data.map { |r| extract_resources_ids(r) }.flatten | ||
|
|
||
| # def validate(data) | ||
| # # Check if duplicate Ids exist for same Resource Type in a data set | ||
| # r_ids = data.map { |r| resources_ids(r) }.flatten | ||
| if resource_ids.uniq == resource_ids | ||
| puts 'No duplicate Ids found. Proceed to evaluate..' | ||
| else | ||
| dup = resource_ids.detect { |r| resource_ids.count(r) > 1 } | ||
| puts "Warning: Found duplicate resource Ids: #{dup}. Please validate Examples before running FHIR Evaluator." | ||
| end | ||
| end | ||
|
|
||
| # if r_ids.uniq == r_ids | ||
| # puts 'No duplicate Ids found. Proceed to evaluate..' | ||
| # else | ||
| # dup = r_ids.detect { |r| r_ids.count(r) > 1 } | ||
| # puts "Warning: Found duplicate resource Ids: #{dup}. Please validate Examples before running FHIR Evaluator." | ||
| # end | ||
| # end | ||
| def summarize(data) | ||
| # @root_resource_ids = data.map { |r| { type: r.resourceType, id: r.id } } | ||
| # @root_bundle_resource_ids = data.map { |r| { type: r.resourceType, id: r.id } if r.resourceType == 'Bundle' } | ||
|
|
||
| # def summarize(data) | ||
| # # @root_resource_ids = data.map { |r| { type: r.resourceType, id: r.id } } | ||
| # # @root_bundle_resource_ids = data.map { |r| { type: r.resourceType, id: r.id } if r.resourceType == 'Bundle' } | ||
| # id_hash = Hash.new { |hash, key| hash[key] = [] } | ||
| # data.map { |e| resources(e) }.flatten.each do |item| | ||
| # id_hash[item[:type]] << item[:id] | ||
| # end | ||
| # @domain_resource_ids = id_hash.to_a | ||
|
|
||
| # # id_hash = Hash.new { |hash, key| hash[key] = [] } | ||
| # # data.map { |e| resources(e) }.flatten.each do |item| | ||
| # # id_hash[item[:type]] << item[:id] | ||
| # # end | ||
| # # @domain_resource_ids = id_hash.to_a | ||
| # @resource_profile_map = data.map { |e| resources_profiles(e) }.flatten.uniq | ||
| # @resource_patient_map = data.map { |e| resources_patients(e) }.flatten.uniq | ||
| # @resource_subject_map = data.map { |e| resources_subjects(e) }.flatten.uniq | ||
| end | ||
|
|
||
| # # @resource_profile_map = data.map { |e| resources_profiles(e) }.flatten.uniq | ||
| # # @resource_patient_map = data.map { |e| resources_patients(e) }.flatten.uniq | ||
| # # @resource_subject_map = data.map { |e| resources_subjects(e) }.flatten.uniq | ||
| # end | ||
| def extract_resources_ids(resource) | ||
| if resource.resourceType == 'Bundle' | ||
| resource.entry.map { |e| extract_resources_ids(e.resource) }.flatten | ||
| else | ||
| "#{resource.resourceType}/#{resource.id}" | ||
| end | ||
| end | ||
|
|
||
| # def resources_ids(resource) | ||
| # if resource.resourceType == 'Bundle' | ||
| # resource.entry.map { |e| resources_ids(e.resource) }.flatten | ||
| # else | ||
| # "#{resource.resourceType}/#{resource.id}" | ||
| # end | ||
| # end | ||
| def resources(resource) | ||
| if resource.resourceType == 'Bundle' | ||
| resource.entry.map { |e| resources(e.resource) }.flatten | ||
| else | ||
| { type: resource.resourceType, id: resource.id } | ||
| end | ||
| end | ||
|
|
||
| # def resources(resource) | ||
| # if resource.resourceType == 'Bundle' | ||
| # resource.entry.map { |e| resources(e.resource) }.flatten | ||
| # else | ||
| # { type: resource.resourceType, id: resource.id } | ||
| # end | ||
| # end | ||
| def extract_resources_profiles(resource) | ||
| if resource.resourceType == 'Bundle' | ||
| resource.entry.map { |e| extract_resources_profiles(e.resource) }.flatten.uniq | ||
| elsif resource.meta&.profile | ||
| { resource_id: resource.id, profile: resource.meta&.profile } | ||
| end | ||
| end | ||
|
|
||
| # def resources_profiles(resource) | ||
| # if resource.resourceType == 'Bundle' | ||
| # resource.entry.map { |e| resources_profiles(e.resource) }.flatten.uniq | ||
| # elsif resource.meta&.profile | ||
| # { resource_id: resource.id, profile: resource.meta&.profile } | ||
| # end | ||
| # end | ||
| def extract_resources_patients(resource) | ||
| if resource.resourceType == 'Bundle' | ||
| resource.entry.map { |e| extract_resources_patients(e.resource) }.flatten.uniq | ||
| elsif defined? resource.patient.reference | ||
| { resource_id: resource.id, patient: resource.patient.reference } | ||
| end | ||
| end | ||
|
|
||
| # def resources_patients(resource) | ||
| # if resource.resourceType == 'Bundle' | ||
| # resource.entry.map { |e| resources_patients(e.resource) }.flatten.uniq | ||
| # elsif defined? resource.patient.reference | ||
| # { resource_id: resource.id, patient: resource.patient.reference } | ||
| # end | ||
| # end | ||
| def extract_resources_subjects(resource) | ||
| if resource.resourceType == 'Bundle' | ||
| resource.entry.map { |e| extract_resources_subjects(e.resource) }.flatten.uniq | ||
| elsif defined? resource.subject.reference | ||
| { resource_id: resource.id, subject: resource.subject.reference } | ||
| end | ||
| end | ||
|
|
||
| # def resources_subjects(resource) | ||
| # if resource.resourceType == 'Bundle' | ||
| # resource.entry.map { |e| resources_subjects(e.resource) }.flatten.uniq | ||
| # elsif defined? resource.subject.reference | ||
| # { resource_id: resource.id, subject: resource.subject.reference } | ||
| # end | ||
| # end | ||
|
|
||
| # def to_json(*_args) | ||
| # { | ||
| # 'Resources' => domain_resource_ids.length, | ||
| # 'Root Resources' => root_resource_ids.length | ||
| # } | ||
| # end | ||
| # end | ||
| def to_json(*_args) | ||
| { | ||
| 'Resources' => domain_resource_ids.length, | ||
| 'Root Resources' => root_resource_ids.length | ||
| } | ||
| end | ||
| end | ||
| end |
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