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with QRDA import
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@dczulada
dczulada committed Nov 10, 2023
1 parent 00c2ab9 commit d9b0651
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Showing 3 changed files with 177 additions and 61 deletions.
34 changes: 16 additions & 18 deletions app/controllers/measures_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -128,24 +128,22 @@ def measurement_period
private

def persist_measure(uploaded_file, permitted_params, user)
logger.tagged(user.harp_id ? user.harp_id : "unknown user") do
measures, main_hqmf_set_id =
if permitted_params[:hqmf_set_id].present?
logger.info("update")
update_measure(uploaded_file: uploaded_file,
target_id: permitted_params[:hqmf_set_id],
value_set_loader: build_vs_loader(permitted_params, false),
user: user)
else
logger.info("create")
create_measure(uploaded_file: uploaded_file,
measure_details: retrieve_measure_details(permitted_params),
value_set_loader: build_vs_loader(permitted_params, false),
user: user)
end
check_measures_for_unsupported_data_elements(measures)
return measures, main_hqmf_set_id
end
measures, main_hqmf_set_id =
if permitted_params[:hqmf_set_id].present?
logger.info("update")
update_measure(uploaded_file: uploaded_file,
target_id: permitted_params[:hqmf_set_id],
value_set_loader: build_vs_loader(permitted_params, false),
user: user)
else
logger.info("create")
create_measure(uploaded_file: uploaded_file,
measure_details: retrieve_measure_details(permitted_params),
value_set_loader: build_vs_loader(permitted_params, false),
user: user)
end
check_measures_for_unsupported_data_elements(measures)
return measures, main_hqmf_set_id
end

def check_measures_for_unsupported_data_elements(measures)
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161 changes: 125 additions & 36 deletions app/controllers/patients_controller.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -250,6 +250,63 @@ def json_export
end
end

# def json_import
# virus_scan params[:patient_import_file]
# is_zip_file params[:patient_import_file]

# # Verify target measure exists
# measure = CQM::Measure.where(id: params[:measure_id]).first
# raise MeasureUpdateMeasureNotFound if measure.nil?

# # Get the JSON files from the zip:
# # meta - contains measure population, patient signature, and troubleshooting meta data.
# # patients - contains the CQM Patients array.
# json = unzip_patient_import_files(params[:patient_import_file])
# meta = JSON.parse(json[:meta])
# raise PatientsModified if meta["patients_signature"].nil?
# raise IncompatibleQdmVersion unless meta["qdm_version"].eql?(APP_CONFIG['support_qdm_version'].to_s)

# # Verify Patients signature hash
# signature = Digest::MD5.hexdigest("#{meta['qdm_version']}#{json[:patients]}")
# raise PatientsModified unless signature.eql?(meta["patients_signature"])

# # Deserialize patients json array to CQM Patient model
# cqm_patients = JSON.parse(json[:patients]).map { |p| CQM::Patient.new.from_json JSON.generate p }

# # Check whether the provided measure populations match the populations in the target measure
# matching_populations = meta["measure_populations"] == measure.population_criteria.keys

# # Prepare patients for insert
# cqm_patients.each do |patient|
# patient[:id] = BSON::ObjectId.new
# patient[:group_id] = current_user.current_group.id
# patient['measure_ids'] = [measure.hqmf_set_id]
# # If the provided populations match the populations in the target measure, include them in the import
# if matching_populations
# patient[:expectedValues].each do |ev|
# ev["measure_id"] = measure.hqmf_set_id
# end
# else
# patient[:expectedValues] = [] # The measure population docs will be inserted when the user saves the patient.
# end
# # Validate patient so we don't have partial inserts
# raise MeasureLoadingOther unless patient.validate
# end

# cqm_patients.each(&:upsert)
# flash[:msg] = {
# title: "QDM PATIENT IMPORT COMPLETED",
# summary: "",
# body: "Your patients have been successfully added to the measure.
# #{'Due to mismatching populations, the Expected Values have been cleared from imported patients.' unless matching_populations}"
# }
# rescue StandardError => e
# puts e.backtrace
# flash[:error] = turn_exception_into_shared_error_if_needed(e).front_end_version
# ensure
# redirect_to "#{root_path}#measures/#{params[:hqmf_set_id]}"
# end

def json_import
virus_scan params[:patient_import_file]
is_zip_file params[:patient_import_file]
Expand All @@ -258,47 +315,25 @@ def json_import
measure = CQM::Measure.where(id: params[:measure_id]).first
raise MeasureUpdateMeasureNotFound if measure.nil?

# Get the JSON files from the zip:
# meta - contains measure population, patient signature, and troubleshooting meta data.
# patients - contains the CQM Patients array.
json = unzip_patient_import_files(params[:patient_import_file])
meta = JSON.parse(json[:meta])
raise PatientsModified if meta["patients_signature"].nil?
raise IncompatibleQdmVersion unless meta["qdm_version"].eql?(APP_CONFIG['support_qdm_version'].to_s)

# Verify Patients signature hash
signature = Digest::MD5.hexdigest("#{meta['qdm_version']}#{json[:patients]}")
raise PatientsModified unless signature.eql?(meta["patients_signature"])

# Deserialize patients json array to CQM Patient model
cqm_patients = JSON.parse(json[:patients]).map { |p| CQM::Patient.new.from_json JSON.generate p }

# Check whether the provided measure populations match the populations in the target measure
matching_populations = meta["measure_populations"] == measure.population_criteria.keys

# Prepare patients for insert
cqm_patients.each do |patient|
patient[:id] = BSON::ObjectId.new
patient[:group_id] = current_user.current_group.id
patient['measure_ids'] = [measure.hqmf_set_id]
# If the provided populations match the populations in the target measure, include them in the import
if matching_populations
patient[:expectedValues].each do |ev|
ev["measure_id"] = measure.hqmf_set_id
end
else
patient[:expectedValues] = [] # The measure population docs will be inserted when the user saves the patient.
end
# Validate patient so we don't have partial inserts
raise MeasureLoadingOther unless patient.validate
vendor_patient_file = File.new(params[:patient_import_file].path)
artifact = Artifact.new(file: vendor_patient_file)

artifact.each do |name, data|
# Add a patient if it passes CDA validation
doc = Nokogiri::XML::Document.parse(data)
doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
patient, _warnings, codes = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
patient.group = current_user.current_group.id
patient.measure_ids << measure.hqmf_set_id
#patient.save
sort_with_descriptions(patient, measure)
end

cqm_patients.each(&:upsert)
flash[:msg] = {
title: "QDM PATIENT IMPORT COMPLETED",
summary: "",
body: "Your patients have been successfully added to the measure.
#{'Due to mismatching populations, the Expected Values have been cleared from imported patients.' unless matching_populations}"
body: "Your patients have been successfully added to the measure."
}
rescue StandardError => e
puts e.backtrace
Expand All @@ -307,6 +342,60 @@ def json_import
redirect_to "#{root_path}#measures/#{params[:hqmf_set_id]}"
end

def sort_with_descriptions(patient, measure)
@code_hash = {}
@valuesets = measure.value_sets.flatten.uniq
@valuesets.each do |vs|
vs.concepts.each do |concept|
@code_hash[key_for_code(concept.code, concept.code_system_oid)] = vs.display_name
end
end
patient.qdmPatient.dataElements.each { |de| add_description_to_data_element(de) }
sorted_elements = patient.qdmPatient.dataElements.sort_by! { |de| data_element_time(de) }.clone
patient.qdmPatient.dataElements.destroy_all
patient.qdmPatient.dataElements << sorted_elements
patient.save
end

def add_description_to_data_element(data_element)
de = data_element
select_negated_code(de) if de['negationRationale'] && de.codes.find { |c| c.system == '1.2.3.4.5.6.7.8.9.10' }
de.codes.each do |code|
display_name = @code_hash[key_for_code(code.code, code.system)]
qdm_status = de.respond_to?(:qdmStatus) ? "#{de.qdmStatus.capitalize}: " : ""
de.description = qdm_status + display_name if display_name
end
return de.description.nil? ? false : true
end

def select_negated_code(data_element)
negated_element = data_element.dataElementCodes.map { |dec| dec if dec[:system] == '1.2.3.4.5.6.7.8.9.10' }.first
negated_vs = negated_element[:code]

valueset = @valuesets.select { |vs| vs[:oid] == negated_vs }
return if valueset.empty?

code = { code: valueset.first.concepts.first['code'], system: valueset.first.concepts.first['code_system_oid'] }
data_element.dataElementCodes << code
end

def key_for_code(code, system)
Digest::SHA2.hexdigest("#{code} #{system}")
end

def data_element_time(data_element)
return data_element['relevantPeriod'][:low] if data_element['relevantPeriod'] && data_element['relevantPeriod'][:low]
return data_element['relevantDatetime'] if data_element['relevantDatetime']
return data_element['prevalencePeriod'][:low] if data_element['prevalencePeriod'] && data_element['prevalencePeriod'][:low]
return data_element['authorDatetime'] if data_element['authorDatetime']
return data_element['resultDatetime'] if data_element['resultDatetime']
return data_element['sentDatetime'] if data_element['sentDatetime']
return data_element['participationPeriod'][:low] if data_element['participationPeriod'] && data_element['participationPeriod'][:low]
return data_element['birthDatetime'] if data_element['birthDatetime']
return data_element['expiredDatetime'] if data_element['expiredDatetime']
return Date.new(2030,1,1) #if ['QDM::PatientCharacteristicEthnicity', 'QDM::PatientCharacteristicRace', 'QDM::PatientCharacteristicSex'].include?(data_element._type)
end

def share_patients
patients = CQM::Patient.by_user(current_user)
patients = patients.where({ :measure_ids.in => [params[:hqmf_set_id]] })
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43 changes: 36 additions & 7 deletions lib/tasks/bonnie_import.rake
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# bundle exec rake bonnie:import:cypress_bundle\[bundle-2023.0.0,[email protected]\]
# bundle exec rake bonnie:import:add_description\[bundle2023@mitre.org\]
# bundle exec rake bonnie:import:sort_entries\[bundle2023@mitre.org\]
# bundle exec rake bonnie:import:add_description\[dczulada@mitre.org\]
# bundle exec rake bonnie:import:sort_entries\[dczulada@mitre.org\]
# bundle exec rake bonnie:import:limit_measures\[[email protected]\]
# bundle exec rake bonnie:import:add_all_measures\[[email protected]\]
# bundle exec rake bonnie:import:export_vs\[[email protected]\]
Expand Down Expand Up @@ -42,6 +42,33 @@ namespace :bonnie do
end
end

task :try_this, [:file] => :setup do |_, args|
vsac_options = {
options: {
profile: 'eCQM Update 2023-05-04'
},
vsac_api_key: '3c4f1c72-0b7f-4a41-9e0e-8e06daaf9bf1',
}
value_set_loader = Measures::VSACValueSetLoader.new(vsac_options)
measure_file = File.new('all-measures/' + args.file)
measure_details = { 'episode_of_care' => 'false' }
loader = Measures::CqlLoader.new(measure_file, measure_details, value_set_loader)
measures = loader.extract_measures
measure_name = File.basename(args.file)


measures.each do |measure|
dirname = 'parsed-measures/' + measure_name
unless File.directory?(dirname)
FileUtils.mkdir_p(dirname)
end
value_sets_json = measure.value_sets.to_json
measure_json = measure.to_json
File.write(dirname + '/' + 'value_sets.json', value_sets_json)
File.write(dirname + '/' + measure_name + '.json', measure_json)
end
end

task :delete_patients, [:email] => :setup do |_, args|
user = User.find_by email: args.email
user.current_group.patients.destroy_all
Expand Down Expand Up @@ -71,12 +98,14 @@ namespace :bonnie do
end
end

task :qrda, [:file, :email, :measure] => :setup do |_, args|
#bundle exec rake bonnie:import:qrda\[patient_file.zip\]
task :qrda, [:file] => :setup do |_, args|
vendor_patient_file = File.new(args.file)
artifact = Artifact.new(file: vendor_patient_file)
user = User.find_by email: args.email
measure = if user.current_group.cqm_measures.where(cms_id: args.measure).first
user.current_group.cqm_measures.where(cms_id: args.measure).first
user = User.find_by email: '[email protected]'
cms_id = 'CMS135v11'
measure = if user.current_group.cqm_measures.where(cms_id: cms_id).first
user.current_group.cqm_measures.where(cms_id: cms_id).first
else
user.current_group.cqm_measures.first
end
Expand All @@ -86,7 +115,7 @@ namespace :bonnie do
doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
patient, _warnings, codes = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
patient.user = user
patient.group = user.current_group
patient.measure_ids << measure.hqmf_set_id
patient.save
end
Expand Down

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