Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Main #22

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Main #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
fa53d2f
Adding activityDefinition
SUHASV117 Jan 14, 2022
d8ca21b
final changes
SUHASV117 Feb 17, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 31 additions & 1 deletion lib/constraints.rb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,9 @@ class Constraints
'one_white' => lambda {|results| results.any? {|bundle| race(bundle) == 'White'}},
'one_black' => lambda {|results| results.any? {|bundle| race(bundle) == 'Black or African American'}},
'one_hispanic' => lambda {|results| results.any? {|bundle| ethnicity(bundle) == 'Hispanic or Latino'}},
'one_smoker' => lambda {|results| results.any? {|bundle| smoker(bundle) }}
'one_smoker' => lambda {|results| results.any? {|bundle| smoker(bundle) }},
'one_hypertension_condition' => lambda {|results| results.any? {|bundle| hypertension_condition(bundle) && observation_diastolic(bundle)}},
'one_hypertension_observation_high' => lambda {|results| results.any? {|bundle| hypertension_observation_high(bundle)}},
}

CONSTRAINTS_MRBURNS = {
Expand All @@ -35,6 +37,8 @@ class Constraints
'one_black',
'one_hispanic',
'one_smoker',
'one_hypertension_condition',
'one_hypertension_observation_high'
]

REQUIRED_PROFILES = [
Expand All @@ -47,6 +51,7 @@ class Constraints
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference',
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter',
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-goal',
'https://hl7.org/fhir/activitydefinition.html',
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-immunization',
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-implantable-device',
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
Expand Down Expand Up @@ -136,6 +141,31 @@ def self.smoker(bundle)
smoking_statuses.map {|status| status.value.text}.include? 'Current every day smoker'
end


def self.hypertension_condition(bundle)
entries = bundle.entry.select {|entry| entry.resource.is_a?(FHIR::Condition)}
conditions = entries.map {|entry| entry.resource}
conditions.map {|condition| condition.code.text}.include? 'Hypertension'
end


def self.observation_diastolic(bundle)
entries = bundle.entry.select {|entry| entry.resource.is_a?(FHIR::Observation)}
observations = entries.map {|entry| entry.resource}
observations.map {|observation| observation&.component&.at(0)&.code&.text.to_s}.include? 'Diastolic Blood Pressure'
end


# 90 <= Diastolic <= 100
def self.hypertension_observation_high(bundle)
entries = bundle.entry.select {|entry| entry.resource.is_a?(FHIR::Observation)}
observations = entries.map {|entry| entry.resource}
hypertension_observation_statuses = observations.select {|observation| observation&.component&.at(0)&.code&.text == 'Diastolic Blood Pressure'}
hypertension_observation_statuses.map {|observation| (observation&.component&.at(0)&.valueQuantity&.value.to_i>=90 && observation&.component&.at(0)&.valueQuantity&.value.to_i<=100) }
end



def self.has(bundle, fhir_class)
bundle.entry.any? {|entry| entry.resource.is_a?(fhir_class)}
end
Expand Down
23 changes: 23 additions & 0 deletions lib/modifications.rb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -373,6 +373,29 @@ def self.modify!(results, random_seed = 3)
goal_provenance.resource.target.last.reference = "urn:uuid:#{goal.id}"
end

=begin
activitydefinition_bundle = results.find { |b| DataScript::Constraints.has(b, FHIR::Activitydefinition) }
unless activitydefinition_bundle
activitydefintion_bundle = results.find { |b| DataScript::Constraints.has(b, FHIR::Patient) }
activitydefinition = FHIR::Activitydefinition.new
activitydefinition.meta = FHIR::Meta.new
activitydefinition.meta.profile = ['https://hl7.org/fhir/activitydefinition.html']
activitydefinition.id = SecureRandom.uuid
activitydefinition.status = 'active'
activitydefinition.description = "controlling hypertension"
goal.subject = { reference: "urn:uuid:#{DataScript::Constraints.patient(goal_bundle).id}" }
goal_target = FHIR::Goal::Target.new
goal_target.dueDate = Time.now.strftime("%Y-%m-%d")
goal.target << goal_target
goal_bundle.entry << create_bundle_entry(goal)
goal_provenance = goal_bundle.entry.find { |e| e.resource.resourceType == 'Provenance' }
goal_provenance.resource.target << FHIR::Reference.new
goal_provenance.resource.target.last.reference = "urn:uuid:#{goal.id}"
end
=end



observation_profiles_valueCodeableConcept_required = [
'http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus'
]
Expand Down
Binary file modified lib/synthea/synthea.jar
View file
Open in desktop
Binary file not shown.
31 changes: 0 additions & 31 deletions uscore-data-script.rb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,6 @@
# Save selections
tik = Time.now.to_i
output_data = 'output/data'
output_validation = 'output/validation'
puts "Overwriting selections into ./#{output_data}"
Dir.mkdir(output_data) unless File.exists?(output_data)
FileUtils.rm Dir.glob("./#{output_data}/*.json")
Expand Down Expand Up @@ -217,10 +216,6 @@
file = File.open(filename,'w:UTF-8')
file.write(json)
file.close
# run FHIR validator on output
puts 'Running FHIR validator on output.'
validation_file = "#{output_validation}/#{patient_bundle_absent_name.entry.first.resource.id}.txt"
system( "java -jar lib/org.hl7.fhir.validator.jar #{filename} -version 4.0.1 -ig hl7.fhir.us.core#3.1.0 > #{validation_file}" )
end

tok = Time.now.to_i
Expand Down Expand Up @@ -263,32 +258,6 @@
FileUtils.rm Dir.glob("./#{output}/**/#{resourceType}.ndjson")
end

# Validating
tik = Time.now.to_i
output_validation = 'output/validation'
puts "Validating... Output logged in ./#{output_validation}"
Dir.mkdir(output_validation) unless File.exists?(output_validation)
FileUtils.rm Dir.glob("./#{output_validation}/*.txt")
selections.each do |bundle|
if bundle.resourceType == 'Bundle'
id = bundle.entry.first.resource.id
else
id = bundle.id
end
# run FHIR validator on output
filename = "#{output_data}/#{id}.json"
validation_file = "#{output_validation}/#{id}.txt"
system( "java -jar lib/org.hl7.fhir.validator.jar #{filename} -version 4.0.1 -ig hl7.fhir.us.core > #{validation_file}" )
end

if patient_bundle_absent_name
filename = "#{output_data}/#{patient_bundle_absent_name.entry.first.resource.id}.json"
# run FHIR validator on output
validation_file = "#{output_validation}/#{patient_bundle_absent_name.entry.first.resource.id}.txt"
system( "java -jar lib/org.hl7.fhir.validator.jar #{filename} -version 4.0.1 -ig hl7.fhir.us.core > #{validation_file}" )
end
tok = Time.now.to_i
puts " Validated #{selections.length + (patient_bundle_absent_name ? 1 : 0)} files (#{DataScript::TimeUtilities.pretty(tok - tik)})."

# Print the amount of time it took...
stop = Time.now.to_i
Expand Down