malawi_hiv_program_reports 1.0.12 → 1.0.13

checksums.yaml

@@ -1,7 +1,7 @@
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data/app/services/malawi_hiv_program_reports/adapters/moh/custom.rb

@@ -86,11 +86,12 @@ module MalawiHivProgramReports
           ActiveRecord::Base.connection.execute <<-SQL
           CREATE TABLE temp_register_start_date (
             patient_id INT NOT NULL,
-            site_id INT DEFAULT NULL,
+            site_id INT NOT NULL,
             start_date DATE NOT NULL,
-            PRIMARY KEY (patient_id)
+            PRIMARY KEY (patient_id, site_id)
           ) #{adapter == 'mysql2' ? 'ENGINE=InnoDB DEFAULT CHARSET=utf8' : ''};
           SQL
+          ActiveRecord::Base.connection.execute 'CREATE INDEX trsd_date ON temp_register_start_date (start_date)'
         end
 
         def exe_temp_order_details_table(adapter:)

data/app/services/malawi_hiv_program_reports/cohort/outcomes.rb

@@ -19,6 +19,8 @@ module MalawiHivProgramReports
 
       def update_cummulative_outcomes
         initialize_table
+        create_tmp_max_drug_orders
+        create_tmp_min_auto_expire_date
 
         # HIC SUNT DRACONIS: The order of the operations below matters,
         # do not change it unless you know what you are doing!!!
@@ -208,7 +210,7 @@ module MalawiHivProgramReports
                 AND voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
             )
             AND patients.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'patient_program.site_id', location: @location)} )
-          GROUP BY patients.patient_id
+          GROUP BY patients.patient_id HAVING cum_outcome = 'Defaulted'
         SQL
       end
 
@@ -237,6 +239,59 @@ module MalawiHivProgramReports
         SQL
       end
 
+      # rubocop:disable Metrics/MethodLength
+      def create_tmp_max_drug_orders
+        date = ActiveRecord::Base.connection.quote(end_date)
+        ActiveRecord::Base.connection.execute 'DROP TABLE IF EXISTS tmp_max_drug_orders'
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE TABLE tmp_max_drug_orders(
+            patient_id INT(11) PRIMARY KEY,
+            start_date DATETIME NOT NULL,
+            site_id INT NOT NULL
+          )
+        SQL
+        ActiveRecord::Base.connection.execute 'CREATE INDEX idx_tmp_max_drug_orders ON tmp_max_drug_orders (patient_id, start_date)'
+        ActiveRecord::Base.connection.execute 'CREATE INDEX tmdo_site_id ON tmp_max_drug_orders (site_id)'
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO tmp_max_drug_orders
+          SELECT o.patient_id, MAX(o.start_date) AS start_date, o.site_id
+          FROM orders o
+          INNER JOIN temp_earliest_start_date tesd ON tesd.patient_id = o.patient_id AND tesd.site_id = o.site_id #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
+          INNER JOIN drug_order ON o.order_id = drug_order.order_id AND quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
+          INNER JOIN arv_drug ad ON ad.drug_id = drug_order.drug_inventory_id
+          WHERE o.order_type_id = #{drug_order_type.order_type_id}
+            AND o.start_date < (DATE(#{date}) + INTERVAL 1 DAY)
+            AND o.voided = 0 #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
+            AND o.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
+          GROUP BY o.patient_id
+        SQL
+      end
+
+      def create_tmp_min_auto_expire_date
+        ActiveRecord::Base.connection.execute 'DROP TABLE IF EXISTS tmp_min_auto_expire_date'
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE TABLE tmp_min_auto_expire_date(
+            patient_id INT(11) PRIMARY KEY,
+            auto_expire_date DATETIME NOT NULL,
+            site_id INT NOT NULL
+          )
+        SQL
+        ActiveRecord::Base.connection.execute 'CREATE INDEX idx_tmp_min_auto_expire_date ON tmp_min_auto_expire_date (patient_id, auto_expire_date)'
+        ActiveRecord::Base.connection.execute 'CREATE INDEX tmaed_site_id ON tmp_min_auto_expire_date (site_id)'
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO tmp_min_auto_expire_date
+          SELECT patient_id, MIN(auto_expire_date) AS auto_expire_date, o.site_id
+          FROM orders o
+          INNER JOIN tmp_max_drug_orders USING (patient_id, start_date, site_id)
+          INNER JOIN drug_order ON o.order_id = drug_order.order_id AND quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
+          INNER JOIN arv_drug ad ON ad.drug_id = drug_order.drug_inventory_id
+          WHERE o.order_type_id = #{drug_order_type.order_type_id}
+            AND o.voided = 0 #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
+          GROUP BY patient_id HAVING auto_expire_date IS NOT NULL
+        SQL
+      end
+      # rubocop:enable Metrics/MethodLength
+
       # Loads all patients who are on treatment
       def load_patients_on_treatment
         date = ActiveRecord::Base.connection.quote(end_date)
@@ -270,35 +325,9 @@ module MalawiHivProgramReports
                    ARV dispensations. In other words filter out any `on ARVs` states whose
                    dispensation's may have been voided or states that were created manually
                    without any drugs being dispensed.  */
-          INNER JOIN (
-            SELECT orders.patient_id, MIN(orders.auto_expire_date) AS auto_expire_date
-            FROM orders
-            INNER JOIN drug_order ON orders.order_id = drug_order.order_id #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
-            INNER JOIN (
-              SELECT patient_id, MAX(start_date) AS start_date
-              FROM orders
-              INNER JOIN drug_order ON orders.order_id = drug_order.order_id #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)} AND drug_order.quantity > 0
-              WHERE order_type_id = #{drug_order_type.order_type_id}
-                AND concept_id IN (#{arv_drugs_concept_set.to_sql})
-                AND orders.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
-                AND voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
-                AND patient_id IN (SELECT patient_id FROM temp_earliest_start_date #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
-                AND patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
-              GROUP BY patient_id
-            ) AS max_drug_orders
-              ON max_drug_orders.patient_id = orders.patient_id
-              AND max_drug_orders.start_date = orders.start_date #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
-            WHERE order_type_id = #{drug_order_type.order_type_id}
-              AND concept_id IN (#{arv_drugs_concept_set.to_sql})
-              AND orders.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
-              AND quantity > 0
-              AND voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
-              AND orders.patient_id IN (SELECT patient_id FROM temp_earliest_start_date #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
-              AND orders.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
-            GROUP BY orders.patient_id
-          ) AS first_order_to_expire
+          INNER JOIN tmp_min_auto_expire_date AS first_order_to_expire
             ON (first_order_to_expire.auto_expire_date >= #{date} OR #{timestampdiff_manager(date1: 'DATE(first_order_to_expire.auto_expire_date)', date2: date, interval: 'DAY')} <= #{@definition == 'pepfar' ? 28 : 56})
-            AND first_order_to_expire.patient_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+            AND first_order_to_expire.patient_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'first_order_to_expire.site_id', location: @location)} #{site_manager(operator: 'AND', column: 'patient_program.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_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
           GROUP BY patients.patient_id #{@adapter == 'mysql2' ? '' : ',patient_state.start_date'}

data/app/services/malawi_hiv_program_reports/cohort/regimens.rb

@@ -9,7 +9,7 @@ module MalawiHivProgramReports
       def patient_regimens(date, location)
         @location = location
         @adapter = ActiveRecord::Base.connection.adapter_name.downcase
-        date = ActiveRecord::Base.connection.quote(date)
+        ActiveRecord::Base.connection.quote(date)
 
         ActiveRecord::Base.connection.select_all <<~SQL
           SELECT prescriptions.patient_id,
@@ -19,33 +19,17 @@ module MalawiHivProgramReports
           FROM (
             SELECT orders.patient_id,
                   #{@adapter == 'mysql2' ? 'GROUP_CONCAT(DISTINCT drug_order.drug_inventory_id ORDER BY drug_order.drug_inventory_id ASC) AS drugs,' : "(SELECT STRING_AGG(drug_inventory_id::VARCHAR, ',') FROM (SELECT DISTINCT drug_order.drug_inventory_id FROM drug_order ORDER BY drug_order.drug_inventory_id ASC) AS subquery) AS drugs,"}
-                   recent_prescription.prescription_date
+                  DATE(tmdo.start_date) prescription_date
             FROM temp_patient_outcomes AS outcomes
+            INNER JOIN tmp_max_drug_orders tmdo ON tmdo.patient_id = outcomes.patient_id AND outcomes.cum_outcome = 'On antiretrovirals' #{site_manager(operator: 'AND', column: 'tmdo.site_id', location: @location)}
             INNER JOIN orders
               ON orders.patient_id = outcomes.patient_id
               AND orders.concept_id IN (#{arv_drugs_concept_set.to_sql})
               AND orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+              AND DATE(orders.start_date) = DATE(tmdo.start_date)
             INNER JOIN drug_order
               ON drug_order.order_id = orders.order_id AND drug_order.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
             /* Only select drugs prescribed on the last prescription day */
-            INNER JOIN (
-              SELECT patient_id, DATE(MAX(start_date)) AS prescription_date
-              FROM orders
-              INNER JOIN drug_order
-                ON drug_order.order_id = orders.order_id
-                AND drug_order.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
-              WHERE orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
-                AND orders.concept_id IN (#{arv_drugs_concept_set.to_sql})
-                AND orders.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
-                AND orders.patient_id IN (
-                  SELECT patient_id FROM temp_patient_outcomes WHERE cum_outcome = 'On antiretrovirals' #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
-                )
-              GROUP BY orders.patient_id
-            ) AS recent_prescription
-              ON recent_prescription.patient_id = orders.patient_id
-              AND orders.start_date
-                BETWEEN recent_prescription.prescription_date
-                AND #{interval_manager(date: 'recent_prescription.prescription_date', value: 1, interval: 'DAY', operator: '+')}
             GROUP BY orders.patient_id #{@adapter == 'mysql2' ? '' : ', recent_prescription.prescription_date'}
           ) AS prescriptions
           LEFT JOIN (

data/app/services/malawi_hiv_program_reports/moh/cohort_builder.rb

@@ -29,9 +29,11 @@ module MalawiHivProgramReports
         drop_temp_register_start_date_table
         drop_temp_other_patient_types
         drop_temp_order_details
+        drop_art_start_date
         create_temp_other_patient_types(end_date)
         create_temp_register_start_date_table(end_date)
         create_temp_order_details(end_date)
+        create_art_start_date(end_date)
         load_data_into_temp_earliest_start_date(end_date.to_date, occupation)
         update_cum_outcome(end_date)
       end
@@ -43,9 +45,11 @@ module MalawiHivProgramReports
         drop_temp_register_start_date_table
         drop_temp_other_patient_types
         drop_temp_order_details
+        drop_art_start_date
         create_temp_other_patient_types(end_date)
         create_temp_register_start_date_table(end_date)
         create_temp_order_details(end_date)
+        create_art_start_date(end_date)
         load_data_into_temp_earliest_start_date(end_date.to_date, occupation)
 
         # create_tmp_patient_table_2(end_date)
@@ -92,7 +96,7 @@ module MalawiHivProgramReports
         cohort_struct.quarterly_all_males = males(quarter_start_date, end_date)
 
         # Pregnant females (all ages)
-        create_temp_pregnant_obs(start_date, end_date)
+        create_temp_pregnant_obs(cum_start_date, end_date)
         cohort_struct.pregnant_females_all_ages = pregnant_females_all_ages(start_date, end_date)
         cohort_struct.cum_pregnant_females_all_ages = pregnant_females_all_ages(cum_start_date, end_date)
         cohort_struct.quarterly_pregnant_females_all_ages = pregnant_females_all_ages(quarter_start_date, end_date)
@@ -678,11 +682,11 @@ module MalawiHivProgramReports
       def load_data_into_temp_cohort_members_table(end_date)
         end_date = ActiveRecord::Base.connection.quote(end_date)
 
-        type_of_patient_concept = concept('Type of patient').concept_id
-        new_patient_concept = concept('New patient').concept_id
-        drug_refill_concept = concept('Drug refill').concept_id
-        external_concept = concept('External Consultation').concept_id
-        program_id = program('HIV program').id
+        concept('Type of patient').concept_id
+        concept('New patient').concept_id
+        concept('Drug refill').concept_id
+        concept('External Consultation').concept_id
+        program('HIV program').id
 
         ActiveRecord::Base.connection.execute <<~SQL
           INSERT INTO temp_cohort_members
@@ -693,7 +697,7 @@ module MalawiHivProgramReports
                  person.birthdate,
                 #{@adapter == 'mysql2' ? 'person.birthdate_estimated' : '(CASE WHEN person.birthdate_estimated = 0 THEN false ELSE true END)'} AS birthdate_estimated,
                  person.death_date,
-                 person.gender, #{
+                 LEFT(person.gender, 1) gender, #{
                    if @adapter == 'mysql2'
                      <<~SQL
                        IF(person.birthdate IS NOT NULL, TIMESTAMPDIFF(YEAR, person.birthdate,  DATE(COALESCE(art_start_date_obs.value_datetime, MIN(art_order.start_date)))), NULL) AS age_at_initiation,
@@ -720,65 +724,21 @@ module MalawiHivProgramReports
                   ORDER BY obs_datetime DESC, date_created DESC LIMIT 1) as reason_for_starting_art,
                  pa.value AS occupation
           FROM patient_program
-          INNER JOIN person ON person.person_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'person.site_id', location: @location)}
+          INNER JOIN person ON person.person_id = patient_program.patient_id AND person.voided = 0 #{site_manager(operator: 'AND', column: 'person.site_id', location: @location)}
           LEFT JOIN (#{current_occupation_query}) pa ON pa.person_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'pa.site_id', location: @location)}
           LEFT JOIN patient_state AS outcome
             ON outcome.patient_program_id = patient_program.patient_program_id #{site_manager(operator: 'AND', column: 'outcome.site_id', location: @location)}
-          LEFT JOIN encounter AS clinic_registration_encounter
-            ON clinic_registration_encounter.encounter_type = (
-              SELECT encounter_type_id FROM encounter_type WHERE LOWER(name) = LOWER('HIV CLINIC REGISTRATION') LIMIT 1
-            )
-            AND clinic_registration_encounter.patient_id = patient_program.patient_id
-            AND clinic_registration_encounter.program_id = patient_program.program_id
-            AND clinic_registration_encounter.encounter_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-            AND clinic_registration_encounter.voided = 0 #{site_manager(operator: 'AND', column: 'clinic_registration_encounter.site_id', location: @location)}
-          LEFT JOIN obs AS art_start_date_obs
-            ON art_start_date_obs.concept_id = 2516
-            AND art_start_date_obs.person_id = patient_program.patient_id
-            AND art_start_date_obs.voided = 0 #{site_manager(operator: 'AND', column: 'art_start_date_obs.site_id', location: @location)}
-            AND art_start_date_obs.obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-            AND art_start_date_obs.encounter_id = clinic_registration_encounter.encounter_id
-           /* TODO: Re-enable the following condition. Has been removed because LLH and PIH
-              were noted to be dropping patients because of it. Seems these sites may have orders
-              without corresponding encounters. Adding this condition bumps up performance a bit. */
-           /* INNER JOIN encounter AS prescription_encounter
-            ON prescription_encounter.patient_id = patient_program.patient_id
-            AND prescription_encounter.program_id = patient_program.program_id
-            AND prescription_encounter.encounter_datetime < DATE(#{end_date}) + INTERVAL 1 DAY
-            AND prescription_encounter.encounter_type IN (SELECT encounter_type_id FROM encounter_type WHERE name LIKE 'Treatment')
-            AND prescription_encounter.voided = 0
-          LEFT JOIN temp_register_start_date AS patient_type_obs
-            ON patient_type_obs.patient_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'patient_type_obs.site_id', location: @location)}
-          INNER JOIN orders AS art_order
-            ON art_order.patient_id = patient_program.patient_id
-            -- AND art_order.encounter_id = prescription_encounter.encounter_id
-            AND art_order.concept_id IN (SELECT concept_id FROM concept_set WHERE concept_set = 1085)
-            AND art_order.start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-            AND art_order.order_type_id = #{order_type('Drug order').id}
-            AND art_order.start_date >= COALESCE(patient_type_obs.start_date, DATE('1901-01-01'))
-            AND art_order.voided = 0 #{site_manager(operator: 'AND', column: 'art_order.site_id', location: @location)}
-          INNER JOIN drug_order
-            ON drug_order.order_id = art_order.order_id
-            AND drug_order.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)} */
+          LEFT JOIN temp_art_start_date AS art_start_date_obs
+            ON art_start_date_obs.patient_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'art_start_date_obs.site_id', location: @location)}
           INNER JOIN temp_order_details AS art_order ON art_order.patient_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'art_order.site_id', location: @location)}
+           AND art_order.start_date <= DATE(#{end_date})
           WHERE patient_program.voided = 0
             AND outcome.voided = 0
             AND patient_program.program_id = 1
             AND outcome.state = 7
             AND outcome.start_date IS NOT NULL #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
-            /*AND patient_program.patient_id NOT IN (
-              SELECT e.patient_id FROM encounter e
-              LEFT JOIN (SELECT * FROM obs WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{new_patient_concept}) AS new_patient ON e.patient_id = new_patient.person_id
-              LEFT JOIN (SELECT * FROM obs WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{drug_refill_concept}) AS refill ON e.patient_id = refill.person_id
-              LEFT JOIN (SELECT * FROM obs WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{external_concept}) AS external ON e.patient_id = external.person_id
-              WHERE e.program_id = #{program_id} AND (refill.value_coded IS NOT NULL OR external.value_coded IS NOT NULL)
-              AND new_patient.value_coded IS NULL
-              AND e.encounter_datetime < DATE(#{end_date}) + INTERVAL 1 DAY
-              AND e.encounter_type IN (SELECT encounter_type_id FROM encounter_type WHERE name = 'REGISTRATION' AND retired = 0)
-              GROUP BY e.patient_id
-            )*/
           GROUP by patient_program.patient_id #{@adapter == 'mysql2' ? '' : ',person.birthdate, person.birthdate_estimated, person.death_date, person.gender, pa.value'}
-          HAVING #{@adapter == 'mysql2' ? 'date_enrolled' : 'art_order.start_date'} <= #{end_date}
+          HAVING reason_for_starting_art IS NOT NULL
         SQL
         remove_drug_refills_and_external_consultation(end_date)
       end
@@ -858,6 +818,44 @@ module MalawiHivProgramReports
         SQL
       end
 
+      def drop_art_start_date
+        ActiveRecord::Base.connection.execute <<~SQL
+          DROP TABLE IF EXISTS temp_art_start_date
+        SQL
+      end
+
+      def create_art_start_date(end_date)
+        ActiveRecord::Base.connection.execute <<-SQL
+          CREATE TABLE temp_art_start_date (
+            patient_id INT(11) NOT NULL,
+            value_datetime DATE NOT NULL,
+            site_id INT(11) NOT NULL,
+            PRIMARY KEY (patient_id)
+          )
+        SQL
+        ActiveRecord::Base.connection.execute 'CREATE INDEX tasd_date ON temp_art_start_date (value_datetime)'
+        ActiveRecord::Base.connection.execute 'CREATE INDEX tasd_site ON temp_art_start_date (site_id)'
+        load_art_start_date(end_date)
+      end
+
+      def load_art_start_date(end_date)
+        ActiveRecord::Base.connection.execute <<-SQL
+          INSERT INTO temp_art_start_date
+          SELECT o.person_id, DATE(MIN(o.value_datetime)) value_datetime, o.site_id
+          FROM encounter e
+          INNER JOIN obs o ON o.encounter_id = e.encounter_id#{' '}
+            AND o.concept_id = 2516#{' '}
+            AND e.encounter_type = 9#{' '}
+            AND e.program_id = 1#{' '}
+            AND e.voided = 0 #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
+            AND e.encounter_datetime < DATE('#{end_date}') + INTERVAL 1 DAY
+            AND o.obs_datetime < (DATE('#{end_date}') + INTERVAL 1 DAY)
+            AND e.voided = 0 #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
+          WHERE e.voided = 0 #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
+          GROUP BY o.person_id
+        SQL
+      end
+
       def create_temp_order_details(end_date)
         exe_temp_order_details_table(adapter: @adapter)
         ActiveRecord::Base.connection.execute <<~SQL
@@ -1001,19 +999,18 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.execute('CREATE INDEX patient_id_site_id_index ON temp_patient_tb_status (patient_id, site_id)')
         ActiveRecord::Base.connection.execute('CREATE INDEX patient_id_tb_status_index ON temp_patient_tb_status (patient_id, tb_status)')
 
+        prepare_latest_tb_status_table
+        create_temp_latest_tb_status(end_date)
+
         ActiveRecord::Base.connection.execute <<~SQL
-          INSERT INTO temp_patient_tb_status (patient_id, tb_status)
-            SELECT e.patient_id, obs.value_coded
-            FROM temp_earliest_start_date e
-            INNER JOIN temp_patient_outcomes o ON o.patient_id = e.patient_id #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
-            RIGHT JOIN obs ON obs.person_id = o.patient_id #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-            WHERE e.date_enrolled <= '#{end_date}' AND obs.obs_datetime <= '#{end_date} 23:59:59'
-            AND LOWER(cum_outcome) = LOWER('On antiretrovirals') AND obs.voided = 0
+          INSERT INTO temp_patient_tb_status
+          SELECT e.person_id, obs.value_coded, e.site_id
+          FROM temp_latest_tb_status e
+          INNER JOIN obs ON obs.person_id = e.person_id AND obs.voided = 0
             AND obs.concept_id = 7459 #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
-            AND obs.obs_datetime = (
-              SELECT MAX(t.obs_datetime) FROM obs t WHERE t.concept_id = 7459 AND t.voided = 0
-              AND t.person_id = e.patient_id AND t.obs_datetime <= '#{end_date} 23:59:59' #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
-            ) GROUP BY e.patient_id #{@adapter == 'mysql2' ? '' : ', obs.value_coded'}
+            AND obs.obs_datetime = e.obs_datetime #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+          #{site_manager(operator: 'WHERE', column: 'e.site_id', location: @location)}
+          GROUP BY e.person_id;
         SQL
       end
 
@@ -1023,6 +1020,34 @@ module MalawiHivProgramReports
 
       private
 
+      def prepare_latest_tb_status_table
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE TABLE IF NOT EXISTS temp_latest_tb_status(
+            person_id INT PRIMARY KEY,
+            obs_datetime DATETIME,
+            site_id INT NOT NULL
+          )
+        SQL
+        unless ActiveRecord::Base.connection.index_exists?(:temp_latest_tb_status, :obs_datetime)
+          ActiveRecord::Base.connection.execute 'CREATE INDEX tlts_date ON temp_latest_tb_status(obs_datetime)'
+        end
+        unless ActiveRecord::Base.connection.index_exists?(:temp_latest_tb_status, :site_id)
+          ActiveRecord::Base.connection.execute 'CREATE INDEX tlts_site ON temp_latest_tb_status(site_id)'
+        end
+        ActiveRecord::Base.connection.execute 'TRUNCATE temp_latest_tb_status'
+      end
+
+      def create_temp_latest_tb_status(end_date)
+        ActiveRecord::Base.connection.select_all <<~SQL
+          INSERT INTO temp_latest_tb_status
+          SELECT t.person_id, MAX(t.obs_datetime) obs_datetime, t.site_id
+          FROM obs t
+          INNER JOIN temp_patient_outcomes o ON o.patient_id = t.person_id AND o.cum_outcome = 'On antiretrovirals' #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)} #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
+          WHERE t.concept_id = 7459 AND t.voided = 0 AND t.obs_datetime <= '#{end_date} 23:59:59' #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
+          GROUP BY t.person_id
+        SQL
+      end
+
       def total_patients_with_screened_bp(total_alive_and_on_art, _start_date, end_date)
         return 0 if total_alive_and_on_art.blank? || total_alive_and_on_art.empty?
 
@@ -1030,23 +1055,13 @@ module MalawiHivProgramReports
                                    .select(:concept_id)
 
         results = ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT o.person_id
-          FROM obs o
-          INNER JOIN (
-            SELECT person_id, MAX(obs.obs_datetime) AS obs_datetime
-            FROM obs
-            WHERE voided = 0 AND concept_id IN (#{bp_concepts.to_sql})
-              AND (value_text IS NOT NULL OR value_numeric IS NOT NULL)
-              AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')} AND obs_datetime >= #{interval_manager(date: end_date, value: 12, interval: 'MONTH', operator: '-')}
-              AND #{in_manager(column: 'person_id', values: total_alive_and_on_art)} #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-            GROUP BY person_id
-          ) AS max_obs
-            ON max_obs.person_id = o.person_id
-            AND max_obs.obs_datetime = o.obs_datetime
-          WHERE o.voided = 0 #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
-            AND o.concept_id IN (#{bp_concepts.to_sql})
-            AND (o.value_text IS NOT NULL OR o.value_numeric IS NOT NULL)
-          GROUP BY o.person_id
+          SELECT person_id
+          FROM obs
+          WHERE voided = 0 AND concept_id IN (#{bp_concepts.to_sql})
+            AND (value_text IS NOT NULL OR value_numeric IS NOT NULL)
+            AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')} AND obs_datetime >= #{interval_manager(date: end_date, value: 12, interval: 'MONTH', operator: '-')}
+            AND #{in_manager(column: 'person_id', values: total_alive_and_on_art)} #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+          GROUP BY person_id
         SQL
 
         ((results.count.to_f / total_alive_and_on_art.count) * 100).to_i
@@ -1139,8 +1154,8 @@ module MalawiHivProgramReports
 
         return [] if patient_ids.blank?
 
-        results = ActiveRecord::Base.connection.select_all(
-          "SELECT ods.patient_id
+        results = ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT ods.patient_id
           FROM orders ods
           INNER JOIN drug_order dos ON ods.order_id = dos.order_id AND ods.voided = 0 #{site_manager(operator: 'AND',
                                                                                                      column: 'dos.site_id', location: @location)}
@@ -1149,21 +1164,8 @@ module MalawiHivProgramReports
           AND #{in_manager(column: 'ods.patient_id', values: patient_ids)}
           AND ods.start_date BETWEEN '#{start_date.to_date.strftime('%Y-%m-%d 00:00:00')}'
           AND '#{end_date.to_date.strftime('%Y-%m-%d 23:59:59')}'
-          AND DATE(ods.start_date) = (SELECT MAX(DATE(o.start_date)) FROM orders o
-                                      INNER JOIN drug_order d ON o.order_id = d.order_id AND o.voided = 0 #{site_manager(
-                                        operator: 'AND', column: 'd.site_id', location: @location
-                                      )}
-                                      WHERE #{in_manager(column: 'o.concept_id',
-                                                         values: [
-                                                           isoniazid_concept_id, pyridoxine_concept_id
-                                                         ])}
-                                      AND o.patient_id = ods.patient_id #{site_manager(operator: 'AND',
-                                                                                       column: 'o.site_id', location: @location)}
-                                      AND d.quantity IS NOT NULL
-                                      AND o.start_date BETWEEN '#{start_date.to_date.strftime('%Y-%m-%d 00:00:00')}'
-                                      AND '#{end_date.to_date.strftime('%Y-%m-%d 23:59:59')}')
-          GROUP BY ods.patient_id"
-        )
+          GROUP BY ods.patient_id
+        SQL
 
         ((results.count.to_f / patient_ids.count) * 100).to_i
       end
@@ -1178,8 +1180,8 @@ module MalawiHivProgramReports
 
         return [] if patient_ids.blank?
 
-        results = ActiveRecord::Base.connection.select_all(
-          "SELECT ods.patient_id
+        results = ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT ods.patient_id
           FROM orders ods
           INNER JOIN drug_order dos ON ods.order_id = dos.order_id AND ods.voided = 0 #{site_manager(operator: 'AND',
                                                                                                      column: 'dos.site_id', location: @location)}
@@ -1188,24 +1190,13 @@ module MalawiHivProgramReports
           AND ods.patient_id in (#{patient_ids.join(',')})
           AND ods.start_date BETWEEN '#{start_date.to_date.strftime('%Y-%m-%d 00:00:00')}'
           AND '#{end_date.to_date.strftime('%Y-%m-%d 23:59:59')}'
-          AND DATE(ods.start_date) = (SELECT MAX(DATE(o.start_date)) FROM orders o
-                                      INNER JOIN drug_order d ON o.order_id = d.order_id AND o.voided = 0 #{site_manager(
-                                        operator: 'AND', column: 'd.site_id', location: @location
-                                      )}
-                                      WHERE o.concept_id =  #{cpt_concept_id} #{site_manager(operator: 'AND',
-                                                                                             column: 'o.site_id', location: @location)}
-                                      AND d.quantity > 0
-                                      AND o.patient_id = ods.patient_id
-                                      AND o.start_date BETWEEN '#{start_date.to_date.strftime('%Y-%m-%d 00:00:00')}'
-                                      AND '#{end_date.to_date.strftime('%Y-%m-%d 23:59:59')}')
-
-          GROUP BY ods.patient_id"
-        )
+          GROUP BY ods.patient_id
+        SQL
 
         ((results.count.to_f / patient_ids.count) * 100).to_i
       end
 
-      def total_breastfeeding_women(_patients_list, total_pregnant_women, _start_date, end_date)
+      def total_breastfeeding_women(_patients_list, total_pregnant_women, _start_date, _end_date)
         total_pregnant_women = if total_pregnant_women.empty?
                                  [0]
                                else
@@ -1228,39 +1219,24 @@ module MalawiHivProgramReports
             ON enc.encounter_id = obs.encounter_id
             AND enc.voided = 0 #{site_manager(operator: 'AND', column: 'enc.site_id', location: @location)}
             AND enc.encounter_type IN (#{encounter_types.to_sql})
+            AND obs.voided = 0 AND obs.concept_id IN (#{breastfeeding_concepts.to_sql}) #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
           INNER JOIN temp_earliest_start_date e
             ON e.patient_id = enc.patient_id #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
             AND LEFT(e.gender, 1) = 'F'
+            AND e.patient_id NOT IN (#{total_pregnant_women.join(',')})
           INNER JOIN temp_patient_outcomes
             ON temp_patient_outcomes.patient_id = e.patient_id #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
             AND temp_patient_outcomes.cum_outcome = 'On antiretrovirals'
-          INNER JOIN (
-            SELECT person_id, MAX(obs_datetime) AS obs_datetime
-            FROM obs
-            INNER JOIN encounter
-              ON encounter.encounter_id = obs.encounter_id
-              AND encounter.encounter_type IN (#{encounter_types.to_sql})
-              AND encounter.voided = 0 #{site_manager(operator: 'AND', column: 'encounter.site_id', location: @location)}
-            WHERE person_id IN (SELECT patient_id FROM temp_patient_outcomes WHERE cum_outcome = 'On antiretrovirals')
-              AND concept_id IN (#{breastfeeding_concepts.to_sql})
-              AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-              AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-            GROUP BY person_id
-          ) AS max_obs
-            ON max_obs.person_id = obs.person_id
-            AND max_obs.obs_datetime = obs.obs_datetime
-          WHERE obs.person_id = e.patient_id
-            AND #{in_manager(column: 'obs.person_id', values: total_pregnant_women.join(','), negation: true)}
-            AND obs.obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-            AND obs.concept_id IN (#{breastfeeding_concepts.to_sql})
-            AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+          INNER JOIN tmp_max_drug_orders AS max_obs ON max_obs.patient_id = obs.person_id
+            AND DATE(max_obs.start_date) = DATE(obs.obs_datetime) #{site_manager(operator: 'AND', column: 'max_obs.site_id', location: @location)}
+          WHERE obs.person_id = e.patient_id #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
           GROUP BY obs.person_id #{@adapter == 'mysql2' ? '' : ', obs.value_coded'}
           HAVING value_coded = 1065
           ORDER BY MAX(obs.obs_datetime) DESC;
         SQL
       end
 
-      def total_pregnant_women(_patients_list, _start_date, end_date)
+      def total_pregnant_women(_patients_list, _start_date, _end_date)
         encounter_types = ::EncounterType.where('LOWER(name) IN (?)',
                                                 ['HIV CLINIC CONSULTATION'.downcase, 'HIV STAGING'.downcase])
                                          .select(:encounter_type_id)
@@ -1272,32 +1248,19 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.select_all <<~SQL
           SELECT obs.person_id, obs.value_coded
           FROM obs obs
-            INNER JOIN encounter enc
-              ON enc.encounter_id = obs.encounter_id
-              AND enc.voided = 0 #{site_manager(operator: 'AND', column: 'enc.site_id', location: @location)}
-              AND enc.encounter_type IN (#{encounter_types.to_sql})
-            INNER JOIN temp_earliest_start_date e
-              ON e.patient_id = enc.patient_id #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
-              AND LEFT(e.gender, 1) = 'F'
+          INNER JOIN encounter enc
+            ON enc.encounter_id = obs.encounter_id
+            AND enc.voided = 0 #{site_manager(operator: 'AND', column: 'enc.site_id', location: @location)}
+            AND enc.encounter_type IN (#{encounter_types.to_sql})
+            AND obs.voided = 0 AND obs.concept_id IN (#{pregnant_concepts.to_sql}) #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+          INNER JOIN temp_earliest_start_date e
+            ON e.patient_id = enc.patient_id #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
+            AND LEFT(e.gender, 1) = 'F'
           INNER JOIN temp_patient_outcomes
             ON temp_patient_outcomes.patient_id = e.patient_id #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
             AND temp_patient_outcomes.cum_outcome = 'On antiretrovirals'
-          INNER JOIN (
-            SELECT person_id, MAX(obs_datetime) AS obs_datetime
-            FROM obs
-            INNER JOIN encounter
-              ON encounter.encounter_id = obs.encounter_id #{site_manager(operator: 'AND', column: 'encounter.site_id', location: @location)}
-              AND encounter.encounter_type IN (#{encounter_types.to_sql})
-              AND encounter.voided = 0
-            WHERE concept_id IN (#{pregnant_concepts.to_sql})
-              AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-              AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-            GROUP BY person_id
-          ) AS max_obs
-            ON max_obs.person_id = obs.person_id
-            AND max_obs.obs_datetime = obs.obs_datetime
-          WHERE obs.concept_id IN (#{pregnant_concepts.to_sql})
-            AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+          INNER JOIN tmp_max_drug_orders AS max_obs ON max_obs.patient_id = obs.person_id
+            AND DATE(max_obs.start_date) = DATE(obs.obs_datetime) #{site_manager(operator: 'AND', column: 'max_obs.site_id', location: @location)}
           GROUP BY obs.person_id #{@adapter == 'mysql2' ? '' : ', obs.value_coded'}
           HAVING obs.value_coded = 1065
           ORDER BY MAX(obs.obs_datetime) DESC;
@@ -1338,28 +1301,13 @@ module MalawiHivProgramReports
       def latest_art_adherence(patients_alive_and_on_art, _start_date, end_date)
         patients_alive_and_on_art = Set.new(patients_alive_and_on_art.map { |patient| patient['patient_id'] })
         end_date = ActiveRecord::Base.connection.quote(end_date)
+        create_tmp_max_adherence(end_date)
 
         not_adherent = ActiveRecord::Base.connection.select_all <<~SQL
           SELECT adherence.person_id
           FROM obs AS adherence
-          INNER JOIN (
-            SELECT obs.person_id, DATE(MAX(obs.obs_datetime)) AS visit_date
-            FROM obs
-            INNER JOIN orders
-              ON orders.order_id = obs.order_id #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
-              AND orders.concept_id IN (#{arv_drug_concepts.to_sql})
-              AND orders.order_type_id = #{drug_order_type.order_type_id}
-              AND orders.voided = 0
-            INNER JOIN temp_patient_outcomes
-              ON temp_patient_outcomes.patient_id = obs.person_id #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
-              AND LOWER(temp_patient_outcomes.cum_outcome) = LOWER('On antiretrovirals')
-            WHERE obs.concept_id = #{drug_order_adherence_concept.concept_id}
-              AND obs.obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-              AND (obs.value_numeric IS NOT NULL OR obs.value_text IS NOT NULL)
-              AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-            GROUP BY obs.person_id
-          ) AS max_adherence
-            ON max_adherence.person_id = adherence.person_id
+          INNER JOIN tmp_max_adherence AS max_adherence
+            ON max_adherence.person_id = adherence.person_id #{site_manager(operator: 'AND', column: 'max_adherence.site_id', location: @location)}
             AND adherence.obs_datetime >= max_adherence.visit_date #{site_manager(operator: 'AND', column: 'adherence.site_id', location: @location)}
             AND adherence.obs_datetime < #{interval_manager(date: 'max_adherence.visit_date', value: 1, interval: 'DAY', operator: '+')}
           INNER JOIN orders
@@ -1383,27 +1331,11 @@ module MalawiHivProgramReports
         adherent = ActiveRecord::Base.connection.select_all <<~SQL
           SELECT adherence.person_id
           FROM obs AS adherence
-          INNER JOIN (
-            SELECT obs.person_id, DATE(MAX(obs.obs_datetime)) AS visit_date
-            FROM obs
-            INNER JOIN orders
-              ON orders.order_id = obs.order_id
-              AND orders.concept_id IN (#{arv_drug_concepts.to_sql})
-              AND orders.order_type_id = #{drug_order_type.order_type_id}
-              AND orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
-            INNER JOIN temp_patient_outcomes
-              ON temp_patient_outcomes.patient_id = obs.person_id #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
-              AND #{in_manager(column: 'temp_patient_outcomes.patient_id', values: not_adherent.blank? ? [0] : not_adherent.join(','), negation: true)}
-              AND LOWER(temp_patient_outcomes.cum_outcome) = LOWER('On antiretrovirals')
-            WHERE obs.concept_id = #{drug_order_adherence_concept.concept_id}
-              AND obs.obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
-              AND (obs.value_numeric IS NOT NULL OR obs.value_text IS NOT NULL)
-              AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-            GROUP BY obs.person_id
-          ) AS max_adherence
-            ON max_adherence.person_id = adherence.person_id
+          INNER JOIN tmp_max_adherence AS max_adherence
+            ON max_adherence.person_id = adherence.person_id #{site_manager(operator: 'AND', column: 'max_adherence.site_id', location: @location)}
             AND adherence.obs_datetime >= max_adherence.visit_date #{site_manager(operator: 'AND', column: 'adherence.site_id', location: @location)}
             AND adherence.obs_datetime < #{interval_manager(date: 'max_adherence.visit_date', value: 1, interval: 'DAY', operator: '+')}
+            AND max_adherence.person_id NOT IN (#{not_adherent.blank? ? 0 : not_adherent.join(',')})
           INNER JOIN orders
             ON orders.order_id = adherence.order_id
             AND orders.order_type_id = #{drug_order_type.order_type_id}
@@ -1424,6 +1356,43 @@ module MalawiHivProgramReports
         [adherent.uniq, not_adherent.uniq, unknown_adherence]
       end
 
+      def create_tmp_max_adherence(end_date)
+        drop_tmp_max_adherence
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE TABLE tmp_max_adherence (
+            person_id INT PRIMARY KEY,
+            visit_date DATE,
+            site_id INT NOT NULL
+          )
+        SQL
+
+        ActiveRecord::Base.connection.execute('CREATE INDEX tma_date ON tmp_max_adherence (visit_date)')
+        ActiveRecord::Base.connection.execute('CREATE INDEX tma_site ON tmp_max_adherence (site_id)')
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO tmp_max_adherence
+          SELECT obs.person_id, DATE(MAX(obs.obs_datetime)) AS visit_date, obs.site_id
+          FROM obs
+          INNER JOIN orders
+            ON orders.order_id = obs.order_id
+            AND orders.concept_id IN (SELECT `concept_set`.`concept_id` FROM `concept_set` WHERE `concept_set`.`concept_set` = 1085)
+            AND orders.order_type_id = 1
+            AND orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+          INNER JOIN temp_patient_outcomes
+            ON temp_patient_outcomes.patient_id = obs.person_id
+            AND temp_patient_outcomes.cum_outcome = 'On antiretrovirals' #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
+          WHERE obs.concept_id = 6987
+            AND obs.obs_datetime < (DATE(#{end_date}) + INTERVAL 1 DAY)
+            AND (obs.value_numeric IS NOT NULL OR obs.value_text IS NOT NULL)
+            AND obs.voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+            GROUP BY obs.person_id;
+        SQL
+      end
+
+      def drop_tmp_max_adherence
+        ActiveRecord::Base.connection.execute('DROP TABLE IF EXISTS tmp_max_adherence')
+      end
+
       def adherence_encounter
         @adherence_encounter ||= encounter_type('ART ADHERENCE')
       end
@@ -1514,9 +1483,8 @@ module MalawiHivProgramReports
           SELECT e.*, s.has_se
           FROM temp_earliest_start_date e
           INNER JOIN temp_patient_side_effects s ON s.patient_id = e.patient_id #{site_manager(operator: 'AND', column: 's.site_id', location: @location)}
-          INNER JOIN temp_patient_outcomes o ON o.patient_id = e.patient_id #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
-          WHERE LOWER(o.cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)}
-          AND DATE(e.date_enrolled) <= '#{end_date.to_date}';
+          INNER JOIN temp_patient_outcomes o ON o.patient_id = e.patient_id AND LOWER(o.cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
+          WHERE DATE(e.date_enrolled) <= '#{end_date.to_date}'  #{site_manager(operator: 'AND', column: 'e.site_id', location: @location)};
         SQL
 
         (records || []).each do |data|
@@ -1631,10 +1599,10 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.select_all <<~SQL
           SELECT t.patient_id
           FROM temp_earliest_start_date t
-          INNER JOIN obs ON t.patient_id = obs.person_id #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)} AND obs.voided = 0
-          WHERE t.date_enrolled BETWEEN '#{start_date}' AND '#{end_date}'
-            AND ((obs.value_coded = #{concept_id} AND obs.concept_id = #{who_stages_criteria}) OR (obs.concept_id = #{concept_id} AND obs.value_coded = #{yes_concept_id}))
-            AND DATE(obs_datetime) <= DATE(date_enrolled) #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
+          INNER JOIN obs ON t.patient_id = obs.person_id
+            AND ((value_coded = #{concept_id} AND concept_id = #{who_stages_criteria}) OR (concept_id = #{concept_id}) AND value_coded = #{yes_concept_id} )
+            AND voided = 0 AND DATE(obs_datetime) <= DATE(date_enrolled) #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+          WHERE t.date_enrolled BETWEEN '#{start_date}' AND '#{end_date}' #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
           GROUP BY patient_id
         SQL
       end
@@ -1650,12 +1618,12 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.select_all <<~SQL
           SELECT t.patient_id
           FROM temp_earliest_start_date t
-          INNER JOIN obs ON t.patient_id = obs.person_id #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
-          WHERE date_enrolled BETWEEN '#{start_date}' AND '#{end_date}'
-          AND ( (#{in_manager(column: 'value_coded', values: [eptb_concept_id, pulmonary_tb_concept_id, current_ptb_concept_id])} AND concept_id = #{who_stages_criteria} )
-            OR#{' '}
+          INNER JOIN obs ON t.patient_id = obs.person_id AND voided = 0
+            AND DATE(obs_datetime) <= DATE(date_enrolled) #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+            AND ( (#{in_manager(column: 'value_coded', values: [eptb_concept_id, pulmonary_tb_concept_id, current_ptb_concept_id])} AND concept_id = #{who_stages_criteria} )
+            OR
               (#{in_manager(column: 'concept_id', values: [eptb_concept_id, pulmonary_tb_concept_id, current_ptb_concept_id])} AND value_coded = #{yes_concept_id}))
-          AND voided = 0 AND DATE(obs_datetime) <= DATE(date_enrolled) #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
+          WHERE date_enrolled BETWEEN '#{start_date}' AND '#{end_date}' #{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
           GROUP BY patient_id
         SQL
       end
@@ -1949,30 +1917,25 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.execute 'DROP TABLE IF EXISTS temp_pregnant_obs;'
         ActiveRecord::Base.connection.execute <<~SQL
           CREATE TABLE temp_pregnant_obs
-          SELECT o.person_id,o.value_coded, o.obs_datetime, o.site_id
+          SELECT o.person_id,o.value_coded, DATE(o.obs_datetime) obs_datetime, o.site_id
           FROM obs o
           WHERE o.concept_id IN (6131,1755,7972,7563)
-            AND o.value_coded IN (1065,1755)#{' '}
+            AND o.value_coded IN (1065,1755)
             AND o.voided = 0 #{site_manager(operator: 'AND', column: 'o.location_id', location: @location)}
             AND o.obs_datetime >= '#{start_date}' AND o.obs_datetime < '#{end_date}' + INTERVAL 1 DAY;
         SQL
         ActiveRecord::Base.connection.execute 'CREATE INDEX fre_person ON temp_pregnant_obs(person_id);'
         ActiveRecord::Base.connection.execute 'CREATE INDEX fre_obs_time ON temp_pregnant_obs(obs_datetime);'
+        ActiveRecord::Base.connection.execute 'CREATE INDEX fre_site ON temp_pregnant_obs(site_id);'
       end
 
       def pregnant_females_all_ages(start_date, end_date)
-        concept('Yes').concept_id
-        concept('IS PATIENT PREGNANT?').concept_id
-        concept('PATIENT PREGNANT').concept_id
-        concept('PREGNANT AT INITIATION?').concept_id
-        concept('Reason for ART eligibility').concept_id
-
         # (patient_id_plus_date_enrolled || []).each do |patient_id, date_enrolled|
         registered = ActiveRecord::Base.connection.select_all <<~SQL
           SELECT tesd.*, ft.value_coded
           FROM temp_earliest_start_date tesd#{' '}
-          INNER JOIN temp_pregnant_obs ft ON ft.person_id = tesd.patient_id AND DATE(ft.obs_datetime) = DATE(tesd.earliest_start_date)
-            AND tesd.gender = 'F'
+          INNER JOIN temp_pregnant_obs ft ON ft.person_id = tesd.patient_id AND ft.obs_datetime = tesd.earliest_start_date
+            AND tesd.gender = 'F' #{site_manager(operator: 'AND', column: 'ft.site_id', location: @location)}
           WHERE tesd.gender = 'F' and tesd.date_enrolled >= DATE('#{start_date}') AND tesd.date_enrolled <= DATE('#{end_date}') #{site_manager(operator: 'AND', column: 'tesd.site_id', location: @location)}
           GROUP BY tesd.patient_id
         SQL
@@ -1983,8 +1946,8 @@ module MalawiHivProgramReports
           WHERE date_enrolled BETWEEN '#{start_date}' AND '#{end_date}'
             AND gender IN ('F','Female') #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
             AND reason_for_starting_art IN (6131,1755,7972,7563)
-          GROUP BY patient_id
         SQL
+
         pregnant_at_initiation_ids = []
         (pregnant_at_initiation || []).each do |patient|
           pregnant_at_initiation_ids << patient['patient_id'].to_i

data/lib/malawi_hiv_program_reports/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module MalawiHivProgramReports
-  VERSION = '1.0.12'
+  VERSION = '1.0.13'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: malawi_hiv_program_reports
 version: !ruby/object:Gem::Version
-  version: 1.0.12
+  version: 1.0.13
 platform: ruby
 authors:
 - Roy Chanunkha
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-20 00:00:00.000000000 Z
+date: 2024-03-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails