Class: MalawiHivProgramReports::Moh::CohortSurvivalAnalysis

Inherits:
Object
  • Object
show all
Defined in:
app/services/malawi_hiv_program_reports/moh/cohort_survival_analysis.rb

Overview

This class is used to add additional cohort disaggregated data rubocop:disable Metrics/ClassLength

Instance Method Summary collapse

Constructor Details

#initialize(name:, type:, start_date:, end_date:, regenerate:, occupation:) ⇒ CohortSurvivalAnalysis

Returns a new instance of CohortSurvivalAnalysis.



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# File 'app/services/malawi_hiv_program_reports/moh/cohort_survival_analysis.rb', line 8

def initialize(name:, type:, start_date:, end_date:, regenerate:, occupation:)
  @name = name
  @type = type
  @start_date = start_date
  @end_date = end_date
  @regenerate = regenerate
  @occupation = occupation
end

Instance Method Details

#append_last_six_months(quarter, results, end_date) ⇒ Object 



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# File 'app/services/malawi_hiv_program_reports/moh/cohort_survival_analysis.rb', line 151

def append_last_six_months(quarter, results, end_date)
  art_service = CohortDisaggregated.new(name: 'survival_analysis',
                                        type: 'survival_analysis', start_date: @start_date.to_date,
                                        end_date: @end_date.to_date, rebuild: @regenerate)

  qstart_date, qend_date = art_service.generate_start_date_and_end_date(quarter)
  qstart_date -= 6.month
  qend_date -= 6.month
  # set_qtr = "Q#{quarter.split(' ')[0][1..1].to_i - 2} #{qend_date.year}"
  set_qtr = (quarter[1..1].to_i - 2)

  set_qtr = (set_qtr.zero? ? 4 : set_qtr)
  set_qtr = (set_qtr == -1 ? 3 : set_qtr)
  set_qtr = (set_qtr == -2 ? 2 : set_qtr)
  set_qtr = "Q#{set_qtr} #{qend_date.year}"

  option_Bplus_women_ids = pregnant_and_breastfeeding_women(qstart_date, qend_date)
  option_Bplus_women_ids = [0] if option_Bplus_women_ids.blank?

  data = ActiveRecord::Base.connection.select_all <<~SQL
    SELECT
      cum_outcome, timestampdiff(month, DATE('#{qend_date}'), DATE('#{end_date}')) qinterval,
      timestampdiff(year, DATE(e.birthdate), DATE('#{end_date}')) AS patient_age,
      e.gender
    FROM temp_earliest_start_date e
    INNER JOIN temp_patient_outcomes o ON o.patient_id = e.patient_id
    WHERE date_enrolled BETWEEN '#{qstart_date.strftime('%Y-%m-%d')}'
    AND '#{qend_date.strftime('%Y-%m-%d')}' AND gender = 'F' AND e.patient_id IN (#{option_Bplus_women_ids.join(', ')});
  SQL

  (data || []).each do |r|
    outcome = r['cum_outcome']
    outcome = (outcome.blank? ? 'Unknown' : outcome)

    if results[set_qtr].blank?
      results[set_qtr] = {}
      results[set_qtr][outcome] = {}
      results[set_qtr][outcome][r['qinterval']] = 0
    elsif results[set_qtr][outcome].blank?
      results[set_qtr][outcome] = {}
      results[set_qtr][outcome][r['qinterval']] = 0
    end

    puts "######### #{r['qinterval']}"
    results[set_qtr][outcome][r['qinterval']] += 1
  end

  results
end

#pregnant_and_breastfeeding_women(start_date, end_date) ⇒ Object 



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# File 'app/services/malawi_hiv_program_reports/moh/cohort_survival_analysis.rb', line 103

def pregnant_and_breastfeeding_women(start_date, end_date)
  patient_ids = []

  patients = ActiveRecord::Base.connection.select_all <<~SQL
    SELECT
      e.*, patient_reason_for_starting_art_text(e.patient_id) reason
    FROM temp_earliest_start_date e
    WHERE date_enrolled BETWEEN '#{start_date.to_date}' AND '#{end_date.to_date}'
    AND gender IN('F','Female') GROUP BY e.patient_id
    HAVING reason LIKE '%pregnant%' OR reason LIKE '%breast%';
  SQL

  (patients || []).each do |aRow|
    patient_ids << aRow['patient_id'].to_i
  end

  concept_ids = []
  ::ConceptName.where(name: 'Breastfeeding').select do |c|
    concept_ids << c.concept_id
  end
  concept_ids << ::ConceptName.find_by_name('Patient pregnant').concept_id
  concept_ids << ::ConceptName.find_by_name('Is patient pregnant?').concept_id
  concept_ids << ::ConceptName.find_by_name('Is patient breast feeding?').concept_id
  yes_concept_id = ::ConceptName.find_by_name('Yes').concept_id

  patients = ActiveRecord::Base.connection.select_all <<~SQL
    SELECT
      e.*, patient_reason_for_starting_art_text(e.patient_id) reason
    FROM temp_earliest_start_date e
    INNER JOIN obs ON obs.person_id = e.patient_id
    WHERE date_enrolled BETWEEN '#{start_date.to_date}' AND '#{end_date.to_date}'
    AND gender IN('F','Female') AND obs.voided = 0
    AND DATE(obs_datetime) = DATE(earliest_start_date)
    AND obs.concept_id IN(#{concept_ids.join(',')})
    AND value_coded = #{yes_concept_id} GROUP BY e.patient_id
    HAVING reason LIKE '%Lymphocyte count below threshold with who stage%'
    ORDER BY obs_datetime DESC;
  SQL

  pregnant_and_breastfeeding_clients = []

  (patients || []).each do |aRow|
    pregnant_and_breastfeeding_clients << aRow['patient_id'].to_i
  end

  (patient_ids + pregnant_and_breastfeeding_clients).uniq
end

#survival_analysis(quarter, age_group) ⇒ Object 



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# File 'app/services/malawi_hiv_program_reports/moh/cohort_survival_analysis.rb', line 17

def survival_analysis(quarter, age_group)
  art_service = CohortDisaggregated.new(name: 'survival_analysis',
                                        type: 'survival_analysis', start_date: Date.today,
                                        end_date: Date.today, rebuild: @regenerate)

  start_date, end_date = art_service.generate_start_date_and_end_date(quarter)
  CohortBuilder.new.init_temporary_tables(start_date, @end_date, @occupation) if @regenerate
  art_service = CohortDisaggregated.new(name: 'survival_analysis',
                                        type: 'survival_analysis', start_date: @start_date.to_date,
                                        end_date: @end_date.to_date, rebuild: @regenerate)

  qtr = quarter.split[0]
  results = {}
  years = 1

  years_to_backto = ActiveRecord::Base.connection.select_one <<~SQL
    SELECT
     TIMESTAMPDIFF(YEAR, DATE(MIN(encounter_datetime)), DATE('#{end_date}')) years
    FROM encounter e WHERE program_id = 1 AND voided = 0;
  SQL

  clinic_start_years = begin
    years_to_backto['years'].to_i
  rescue StandardError
    nil
  end
  clinic_start_years = 10 if clinic_start_years.blank?

  while years < clinic_start_years
    yr = (quarter.split[1].to_i - years)
    set_qtr = "#{qtr} #{yr}"
    qstart_date, qend_date = art_service.generate_start_date_and_end_date(set_qtr)
    results[set_qtr] = {}

    case age_group
    when 'General'
      additional_sql = ' GROUP BY e.patient_id'
    when 'Children'
      additional_sql = ' GROUP BY e.patient_id'
      additional_sql += ' HAVING patient_age < 15'
    when 'Women'
      option_Bplus_women_ids = pregnant_and_breastfeeding_women(qstart_date, qend_date)

      option_Bplus_women_ids = [0] if option_Bplus_women_ids.blank?

      additional_sql = " AND e.patient_id IN (#{option_Bplus_women_ids.join(', ')})"
      additional_sql += ' GROUP BY e.patient_id'
      additional_sql += ' HAVING patient_age >= 15'
      additional_sql += ' AND gender = "F"'
    end

    begin
      data = ActiveRecord::Base.connection.select_all <<~SQL
        SELECT
          cum_outcome, timestampdiff(month, DATE('#{qend_date}'), DATE('#{end_date}')) qinterval,
          timestampdiff(year, DATE(e.birthdate), DATE('#{end_date}')) AS patient_age,
          e.gender
        FROM temp_earliest_start_date e
        INNER JOIN temp_patient_outcomes o ON o.patient_id = e.patient_id
        WHERE date_enrolled BETWEEN '#{qstart_date.strftime('%Y-%m-%d')}'
        AND '#{qend_date.strftime('%Y-%m-%d')}'
        #{additional_sql};
      SQL
    rescue StandardError
      return results
    end

    (data || []).each do |r|
      outcome = r['cum_outcome']
      outcome = (outcome.blank? ? 'Unknown' : outcome)

      if results[set_qtr][outcome].blank?
        results[set_qtr][outcome] = {}
        results[set_qtr][outcome][r['qinterval']] = 0
      end
      results[set_qtr][outcome][r['qinterval']] += 1
    end

    years += 1
  end

  append_last_six_months(quarter, results, end_date) if age_group == 'Women'

  results
end