Class: MalawiHivProgramReports::Cohort::SideEffects
Instance Method Summary
collapse
#cast_manager, #current_partition, #exe_create_drill_down_table, #exe_temp_cohort_members_table, #exe_temp_order_details_table, #exe_temp_other_patient_types, #exe_temp_register_start_date_table, #exe_tmp_patient_table, #function_manager, #group_by_columns, #in_manager, #interval_manager, #min_filt, #site_manager, #timestampdiff_manager
#concept, #concept_id_to_name, #concept_name, #concept_name_to_id, #drug, #encounter_type, #global_property, #order_type, #patient_identifier_type, #program, #report_type, #user_property
Instance Method Details
#art_side_effects ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 136
def art_side_effects
@art_side_effects ||= concept_name('Malawi ART Side Effects')
end
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#initialize_table ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 19
def initialize_table
ActiveRecord::Base.connection.execute <<~SQL
DROP TABLE IF EXISTS temp_patient_side_effects
SQL
ActiveRecord::Base.connection.execute <<~SQL
CREATE TABLE temp_patient_side_effects (
patient_id INT PRIMARY KEY,
has_se VARCHAR(120) NOT NULL,
site_id INT DEFAULT NULL
)
SQL
ActiveRecord::Base.connection.execute 'CREATE INDEX tpse_site_id ON temp_patient_side_effects(site_id)'
ActiveRecord::Base.connection.execute 'CREATE INDEX idx_se ON temp_patient_side_effects(has_se)'
ActiveRecord::Base.connection.execute <<~SQL
CREATE INDEX idx_side_effects ON temp_patient_side_effects (patient_id, has_se, site_id)
SQL
end
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#load_patients_missing_side_effects(date) ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 117
def load_patients_missing_side_effects(date)
date = ActiveRecord::Base.connection.quote(date)
ActiveRecord::Base.connection.execute <<~SQL
INSERT INTO temp_patient_side_effects
SELECT patient_id, 'Unknown', #{@location} FROM temp_earliest_start_date
WHERE date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
AND patient_id NOT IN (SELECT patient_id FROM temp_patient_side_effects #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
SQL
end
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#load_patients_with_side_effects(date) ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 38
def load_patients_with_side_effects(date)
date = ActiveRecord::Base.connection.quote(date)
ActiveRecord::Base.connection.execute <<~SQL
INSERT INTO temp_patient_side_effects(patient_id, has_se, site_id)
SELECT patients.patient_id, 'Yes', #{@location}
FROM temp_earliest_start_date AS patients
INNER JOIN temp_patient_outcomes
ON temp_patient_outcomes.patient_id = patients.patient_id
AND LOWER(temp_patient_outcomes.cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
INNER JOIN obs AS side_effects_group
ON side_effects_group.person_id = patients.patient_id
AND side_effects_group.concept_id = #{art_side_effects.concept_id}
AND side_effects_group.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects_group.site_id', location: @location)}
/* Limit check to last visit before #{date} */
INNER JOIN (
SELECT person_id, MAX(obs_datetime) AS obs_datetime FROM obs
WHERE concept_id = #{art_side_effects.concept_id}
/* Side effects on initial visit are treated as contra-indications */
AND obs_datetime < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
AND voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
AND person_id IN (SELECT patient_id FROM temp_patient_outcomes WHERE LOWER(cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'site_id', location: @location)})
GROUP BY person_id
) AS last_visit
ON last_visit.person_id = side_effects_group.person_id
AND last_visit.obs_datetime = side_effects_group.obs_datetime
AND last_visit.obs_datetime >= #{interval_manager(date: 'patients.date_enrolled', value: 1, interval: 'DAY', operator: '+')}
INNER JOIN obs AS side_effects
ON side_effects.person_id = patients.patient_id
AND side_effects_group.obs_id = side_effects.obs_group_id
AND side_effects.value_coded = #{yes.concept_id}
AND side_effects.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects.site_id', location: @location)}
WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
GROUP BY patients.patient_id
SQL
end
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#load_patients_without_side_effects(date) ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 75
def load_patients_without_side_effects(date)
date = ActiveRecord::Base.connection.quote(date)
ActiveRecord::Base.connection.execute <<~SQL
INSERT INTO temp_patient_side_effects
SELECT patients.patient_id, 'No', #{@location}
FROM temp_earliest_start_date AS patients
INNER JOIN temp_patient_outcomes
ON temp_patient_outcomes.patient_id = patients.patient_id
AND LOWER(temp_patient_outcomes.cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
INNER JOIN obs AS side_effects_group
ON side_effects_group.person_id = patients.patient_id
AND side_effects_group.concept_id = #{art_side_effects.concept_id}
AND side_effects_group.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects_group.site_id', location: @location)}
/* Limit check to last visit before #{date} */
INNER JOIN (
SELECT person_id, MAX(obs_datetime) AS obs_datetime FROM obs
WHERE concept_id = #{art_side_effects.concept_id}
/* Side effects on initial visit are treated as contra-indications */
AND obs_datetime < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
AND voided = 0 #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
AND person_id IN (
SELECT patient_id FROM temp_patient_outcomes WHERE LOWER(cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
)
GROUP BY person_id
) AS last_visit
ON last_visit.person_id = side_effects_group.person_id
AND last_visit.obs_datetime = side_effects_group.obs_datetime
AND last_visit.obs_datetime >= #{interval_manager(date: 'patients.date_enrolled', value: 1, interval: 'DAY', operator: '+')}
INNER JOIN obs AS side_effects
ON side_effects.person_id = patients.patient_id
AND side_effects_group.obs_id = side_effects.obs_group_id
AND side_effects.value_coded = #{no.concept_id}
AND side_effects.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects.site_id', location: @location)}
WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
AND patients.patient_id NOT IN (
SELECT patient_id FROM temp_patient_side_effects WHERE has_se = 'Yes' #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
)
GROUP BY patients.patient_id
SQL
end
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#no ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 132
def no
@no ||= concept_name('No')
end
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#update_side_effects(date, location) ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 9
def update_side_effects(date, location)
@location = location
@adapter = ActiveRecord::Base.connection.adapter_name.downcase
initialize_table
load_patients_with_side_effects(date)
load_patients_without_side_effects(date)
load_patients_missing_side_effects(date)
end
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#yes ⇒ Object
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# File 'app/services/malawi_hiv_program_reports/cohort/side_effects.rb', line 128
def yes
@yes ||= concept_name('Yes')
end
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