Module: MalawiHivProgramReports::Pepfar::Utils

Included in:
ArvRefillPeriods, Clinic::TptOutcome, Cohort::Disaggregated, MaternalStatus, PatientStartVl, TbPrev2, TbPrev3, TptStatus, TxCurrMmd, TxMl, TxNew, TxRtt, TxTb, ViralLoadCoverage, ViralLoadCoverage2
Defined in:
app/services/malawi_hiv_program_reports/pepfar/utils.rb

Overview

Common utilities for Pepfar reports

Constant Summary collapse

COHORT_REGIMENS = 
%w[
  0P 2P 4PP 4PA 9PP 9PA 11PP 11PA 12PP 12PA 14PP 14PA 15PP 15PA 16P 17PP 17PA
  4A 5A 6A 7A 8A 9A 10A 11A 12A 13A 14A 15A 16A 17A
].freeze
FULL_6H_COURSE_PILLS = 
146
FULL_3HP_COURSE_DAYS = 
12.days

Instance Method Summary collapse

Instance Method Details

#drug_refills_and_external_consultation_list ⇒ Object

this just gives all clients who are truly external or drug refill rubocop:disable Metrics/MethodLength rubocop:disable Metrics/AbcSize



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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 93

def drug_refills_and_external_consultation_list
  to_remove = [0]

  type_of_patient_concept = ::ConceptName.find_by_name('Type of patient').concept_id
  new_patient_concept = ::ConceptName.find_by_name('New patient').concept_id
  drug_refill_concept = ::ConceptName.find_by_name('Drug refill').concept_id
  external_concept = ::ConceptName.find_by_name('External consultation').concept_id
  hiv_clinic_registration_id = ::EncounterType.find_by_name('HIV CLINIC REGISTRATION').encounter_type_id

  res = ActiveRecord::Base.connection.select_all <<~SQL
    SELECT p.person_id patient_id
    FROM person #{current_partition} p
    INNER JOIN patient_program #{current_partition} pp ON pp.patient_id = p.person_id AND pp.program_id = #{::Program.find_by_name('HIV PROGRAM').id} AND pp.voided = 0
    INNER JOIN patient_state #{current_partition} ps ON ps.patient_program_id = pp.patient_program_id AND ps.state = 7 AND ps.start_date IS NOT NULL
    LEFT JOIN encounter #{current_partition} as hiv_registration ON hiv_registration.patient_id = p.person_id AND hiv_registration.encounter_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) AND hiv_registration.encounter_type = #{hiv_clinic_registration_id} AND hiv_registration.voided = 0
    LEFT JOIN (
      SELECT * FROM obs #{current_partition} WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{new_patient_concept} AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
    ) AS new_patient ON p.person_id = new_patient.person_id
    LEFT JOIN (
      SELECT * FROM obs #{current_partition} WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{drug_refill_concept} AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
      ) AS refill ON p.person_id = refill.person_id
    LEFT JOIN (
      SELECT * FROM obs #{current_partition} WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{external_concept} AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
      ) AS external ON p.person_id = external.person_id
    WHERE (refill.value_coded IS NOT NULL OR external.value_coded IS NOT NULL)
    AND NOT (hiv_registration.encounter_id IS NOT NULL OR new_patient.value_coded IS NOT NULL)
    GROUP BY p.person_id
    ORDER BY hiv_registration.encounter_datetime DESC, refill.obs_datetime DESC, external.obs_datetime DESC
  SQL
  res.each do |record|
    to_remove << record['patient_id'].to_i
  end
  to_remove.join(',')
end

#isoniazid_rifapentine_concept ⇒ Object 



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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 134

def isoniazid_rifapentine_concept
  @isoniazid_rifapentine_concept ||= ::ConceptName.find_by!(name: 'Isoniazid/Rifapentine')
end

#patient_completed_tpt?(patient, tpt) ⇒ Boolean

Returns whether a patient completed their course of TPT

Returns:

  • (Boolean) 


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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 77

def patient_completed_tpt?(patient, tpt)
  if tpt == '3HP'
    # return true if patient['total_days_on_medication'].to_i >= 83 # 3 months
    return true if patient['months_on_tpt'].to_i >= 3

    divider = patient['drug_concepts'].split(',').length > 1 ? 14.0 : 7.0
    days_on_medication = (patient['total_days_on_medication'] / divider).round
    days_on_medication.days >= FULL_3HP_COURSE_DAYS
  else
    patient['total_days_on_medication'].to_i >= FULL_6H_COURSE_PILLS
  end
end

#patient_on_3hp?(patient) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 138

def patient_on_3hp?(patient)
  drug_concepts = patient['drug_concepts'].split(',').collect(&:to_i)
  drug_concepts.intersect?([rifapentine_concept.concept_id, isoniazid_rifapentine_concept&.concept_id])
end

#patient_on_tb_treatment?(patient_id) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 143

def patient_on_tb_treatment?(patient_id)
  ::Observation.where(person_id: patient_id, concept_id: ::ConceptName.find_by_name('TB status').concept_id,
                      value_coded: ::ConceptName.find_by_name('Confirmed TB on treatment').concept_id)
               .where("obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY',
                                                         operator: '+')}").exists?
end

#pepfar_age_groups ⇒ Object

An array of all groups as required by Pepfar.



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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 10

def pepfar_age_groups
  @pepfar_age_groups ||= [
    'Unknown',
    '<1 year',
    '1-4 years', '5-9 years',
    '10-14 years', '15-19 years',
    '20-24 years',
    '25-29 years', '30-34 years',
    '35-39 years', '40-44 years',
    '45-49 years', '50-54 years',
    '55-59 years', '60-64 years',
    '65-69 years', '70-74 years',
    '75-79 years', '80-84 years',
    '85-89 years',
    '90 plus years'
  ].freeze
end

#pepfar_patient_drilldown_information(patients, current_date) ⇒ Object

Returns the drilldown information for all specified patients (ie patient_ids)

Information returned for a patient is as follows:

* patient_id
* arv_number or filing_number
* age_group
* birthdate
* gender

Raises:

  • (::ArgumentError) 


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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 42

def pepfar_patient_drilldown_information(patients, current_date)
  raise ::ArgumentError, "current_date can't be nil" unless current_date

  ::Person.joins("LEFT JOIN patient_identifier #{current_partition} ON patient_identifier.patient_id = person.person_id
                    AND patient_identifier.voided = 0
                    AND patient_identifier.identifier_type IN (#{pepfar_patient_identifier_type.to_sql})")
          .where(person_id: patients)
          .select("person.person_id AS patient_id,
                   person.gender,
                   person.birthdate,
                   disaggregated_age_group(person.birthdate, DATE(#{ActiveRecord::Base.connection.quote(current_date)})) AS age_group,
                   patient_identifier.identifier AS arv_number")
end

#pepfar_patient_identifier_type ⇒ Object

Returns the preferred Pepfar identifier type.

In some clinics like Lighthouse Filing numbers are used exclusively and in other sites, ARV Numbers are used.



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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 61

def pepfar_patient_identifier_type
  name = GlobalProperty.find_by(property: 'use.filing.numbers')&.property_value
  name = name.present? && name == 'true' ? 'Filing number' : 'ARV Number'
  ::PatientIdentifierType.where(name:).select(:patient_identifier_type_id)
end

#rifapentine_concept ⇒ Object

rubocop:enable Metrics/MethodLength rubocop:enable Metrics/AbcSize



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# File 'app/services/malawi_hiv_program_reports/pepfar/utils.rb', line 130

def rifapentine_concept
  @rifapentine_concept ||= ::ConceptName.find_by!(name: 'Rifapentine')
end