malawi_hiv_program_reports 1.1.3 → 1.1.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ed231eff9bb9c45a7d57027366c82fc112fc1de0cb6c4f457cd87bfeed1bd908
-  data.tar.gz: 3b9a9292285146cac5a4f202bf2d2266fdf323f1acdb67a94706efee322f4afe
+  metadata.gz: df87fea0cc11ac0afae293f935d62c7f6c79a8e487e1ae0161d2e9e18b87e843
+  data.tar.gz: 9f1d344482d7f661d83f4140734f7339b81071e9984b20e25ed3af5e9c391bae
 SHA512:
-  metadata.gz: 2dab0b971e5a76b0097586837b7adb5869d5c0d34563824cc79d02b8cce0679f22a1afce0955b3a733663e017a6886ccced14f924dd5636f34026c05fc6649b4
-  data.tar.gz: 7015b44578a5bdfaea8a15c2b85b03823688b5a13fdf37e683612549c257376c0583117a28b03332d4af53c2561069c1b5d406862fd341ba15e0c724b0bbdfe7
+  metadata.gz: bead67daba89758fba7d271bfc729b0455e85a88edc1ae382ed17436bd2e67b6088df8b3d8ce181cbdb6457331c4c4fe3caef0b9fefd102bb66300ee9335c32d
+  data.tar.gz: d615b55bb62b59ed7eb3bd14d20ac8fb7ace2e04ec3dcbc8df2badcc3dce8ac370a96123471e6ac0403505810231914abb1ac3ee806183720be6e5c5fbceb29a

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

@@ -66,6 +66,7 @@ module MalawiHivProgramReports
         # HIC SUNT DRACONIS: The order of the operations below matters,
         # do not change it unless you know what you are doing!!!
         load_patients_who_died(start:)
+        load_other_patient_who_died(start:)
         load_patients_who_stopped_treatment(start:)
         load_patients_without_drug_orders(start:)
         load_patients_on_treatment(start:)
@@ -94,7 +95,7 @@ module MalawiHivProgramReports
             AND drug_order.site_id = o.site_id AND drug_order.quantity > 0
             AND drug_order.drug_inventory_id IN (#{arv_drug})
           WHERE o.order_type_id = 1 -- drug order
-            AND o.start_date < (DATE(#{start ? start_date : end_date}) + INTERVAL 1 DAY)
+            AND o.start_date < (DATE(#{start ? start_date : end_date}) #{start ? '' : '+ INTERVAL 1 DAY'})
             AND o.voided = 0
           GROUP BY o.patient_id
           ON DUPLICATE KEY UPDATE start_date = VALUES(start_date), min_order_date = VALUES(min_order_date)
@@ -110,8 +111,8 @@ module MalawiHivProgramReports
           INNER JOIN drug_order PARTITION (p#{location}) ON drug_order.order_id = o.order_id AND drug_order.quantity > 0
             AND drug_order.drug_inventory_id IN (#{arv_drug})
           WHERE o.order_type_id = 1 -- drug order
-            AND o.start_date < (DATE(#{start ? start_date : end_date}) + INTERVAL 1 DAY)
-            AND o.start_date >= (DATE(#{start ? prev_date : start_date}) + INTERVAL 1 DAY)
+            AND o.start_date < (DATE(#{start ? start_date : end_date}) #{start ? '' : '+ INTERVAL 1 DAY'})
+            AND o.start_date >= (DATE(#{start ? prev_date : start_date}) #{start ? '' : '+ INTERVAL 1 DAY'})
             AND o.voided = 0
           GROUP BY o.patient_id
           ON DUPLICATE KEY UPDATE start_date = VALUES(start_date), min_order_date = VALUES(min_order_date)
@@ -185,7 +186,7 @@ module MalawiHivProgramReports
           SELECT pp.patient_id, #{location}, MAX(ps.start_date) start_date
           FROM patient_state PARTITION (p#{location}) AS ps
           INNER JOIN patient_program PARTITION (p#{location}) AS pp ON pp.patient_program_id = ps.patient_program_id AND pp.program_id = 1 AND pp.voided = 0
-          WHERE ps.start_date < DATE(#{end_date}) + INTERVAL 1 DAY
+          WHERE ps.start_date < DATE(#{start ? start_date : end_date}) #{start ? '' : '+ INTERVAL 1 DAY'}
             AND ps.voided = 0 AND pp.patient_id IN (SELECT patient_id FROM cdr_temp_cohort_members PARTITION (p#{location}))
           GROUP BY pp.patient_id
           HAVING start_date IS NOT NULL
@@ -228,28 +229,28 @@ module MalawiHivProgramReports
       def load_patients_who_died(start: false)
         ActiveRecord::Base.connection.execute <<~SQL
           INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
-          SELECT patients.patient_id, 'Patient died', patient_state.start_date, #{location}, 1
-          FROM cdr_temp_cohort_members PARTITION (p#{location}) AS patients
-          INNER JOIN patient_program PARTITION (p#{location})
-            ON patient_program.patient_id = patients.patient_id
-            AND patient_program.program_id = 1
-            AND patient_program.voided = 0
-          INNER JOIN patient_state PARTITION (p#{location})
-            ON patient_state.patient_program_id = patient_program.patient_program_id
-            AND patient_state.state = (#{program_states('Patient died').limit(1).to_sql})
-            AND patient_state.start_date < DATE(#{end_date}) + INTERVAL 1 DAY
-            AND patient_state.voided = 0
-          WHERE patients.date_enrolled <= DATE(#{end_date})
-          AND patient_state.date_created = (
-            SELECT MAX(date_created)
-            FROM patient_state PARTITION (p#{location}) ps
-            WHERE ps.patient_program_id = patient_state.patient_program_id
-            AND ps.state = patient_state.state AND ps.voided = 0 AND ps.start_date <= #{end_date})
+          SELECT patients.patient_id, 'Patient died', patients.outcome_date, #{location}, 1
+          FROM cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location}) AS patients
+          WHERE patients.outcomes = 1 AND patients.cum_outcome = 'Patient died'
           GROUP BY patients.patient_id
           ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
         SQL
       end
 
+      def load_other_patient_who_died(start: false)
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
+          SELECT tesd.patient_id, 'Patient died', MAX(ps.start_date), #{location}, 1
+          FROM cdr_temp_cohort_members PARTITION (p#{location}) tesd
+          INNER JOIN patient_program PARTITION (p#{location}) pp ON pp.patient_id = tesd.patient_id AND pp.program_id = 1 AND pp.voided = 0
+          INNER JOIN patient_state PARTITION (p#{location}) ps ON ps.patient_program_id = pp.patient_program_id AND ps.state = 3 AND ps.voided = 0 AND ps.start_date <= #{end_date}
+          WHERE tesd.patient_id NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location}) WHERE step = 1)
+          AND tesd.date_enrolled < DATE(#{start ? start_date : end_date}) #{start ? '' : '+ INTERVAL 1 DAY'}
+          GROUP BY tesd.patient_id
+          ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
+        SQL
+      end
+
       # Loads all patients with an outcome of transferred out or
       # treatment stopped into temp_patient_outcomes table.
       def load_patients_who_stopped_treatment(start: false)
@@ -278,7 +279,7 @@ module MalawiHivProgramReports
           INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
           SELECT patients.patient_id, 'Unknown', NULL, #{location}, 3
           FROM cdr_temp_cohort_members PARTITION (p#{location}) AS patients
-          WHERE date_enrolled <= #{end_date}
+          WHERE date_enrolled < DATE(#{start ? start_date : end_date}) #{start ? '' : '+ INTERVAL 1 DAY'}
             AND (patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location}) WHERE step IN (1, 2, 3, 4))
             AND (patient_id) NOT IN (SELECT patient_id FROM cdr_temp_max_drug_orders#{start ? '_start' : ''} PARTITION (p#{location}))
           ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
@@ -292,7 +293,7 @@ module MalawiHivProgramReports
           SELECT patients.patient_id, 'On antiretrovirals', COALESCE(cs.outcome_date, patients.start_date), #{location}, 4
           FROM cdr_temp_min_auto_expire_date#{start ? '_start' : ''} PARTITION (p#{location}) AS patients
           LEFT JOIN cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location}) AS cs ON cs.patient_id = patients.patient_id AND cs.site_id = patients.site_id
-          WHERE patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} > #{end_date}
+          WHERE patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} > DATE(#{start ? start_date : end_date}) #{start ? '- INTERVAL 1 DAY' : ''}
           AND (patients.patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location}) WHERE step IN (1, 2, 3))
           ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
         SQL
@@ -304,7 +305,7 @@ module MalawiHivProgramReports
           SELECT patients.patient_id, 'Defaulted', patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'},#{location}, 5
           FROM cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location}) AS patients
           LEFT JOIN cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location}) AS cs ON cs.patient_id = patients.patient_id
-          WHERE patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} <= #{end_date}
+          WHERE patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} <= DATE(#{start ? start_date : end_date}) #{start ? '- INTERVAL 1 DAY' : ''}
           AND (patients.patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location}) WHERE step IN (1, 2, 3, 4))
           ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
         SQL
@@ -314,7 +315,7 @@ module MalawiHivProgramReports
       def load_defaulters(start: false)
         ActiveRecord::Base.connection.execute <<~SQL
           INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
-          SELECT patient_id, #{patient_outcome_function('patient_id', 'site_id')}, NULL, #{location}, 6
+          SELECT patient_id, #{patient_outcome_function('patient_id', 'site_id', start)}, NULL, #{location}, 6
           FROM cdr_temp_cohort_members PARTITION (p#{location})
           WHERE date_enrolled <= #{end_date}
           AND (patient_id, site_id) NOT IN (SELECT patient_id, site_id FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location}) WHERE step IN (1, 2, 3, 4, 5))
@@ -325,10 +326,10 @@ module MalawiHivProgramReports
       # ===================================
       #  Function Management Region
       # ===================================
-      def patient_outcome_function(sql_column, site_id)
+      def patient_outcome_function(sql_column, site_id, start)
         case definition
-        when 'moh' then "patient_outcome(#{sql_column}, #{end_date}, #{site_id})"
-        when 'pepfar' then "pepfar_patient_outcome(#{sql_column}, #{end_date}, #{site_id})"
+        when 'moh' then "patient_outcome(#{sql_column}, #{start ? "'#{start_date.to_date - 1.day}'" : end_date}, #{site_id})"
+        when 'pepfar' then "pepfar_patient_outcome(#{sql_column}, #{start ? "'#{start_date.to_date - 1.day}'" : end_date}, #{site_id})"
         else raise "Invalid outcomes definition: #{definition}"
         end
       end

data/app/services/malawi_hiv_program_reports/pepfar/viral_load_coverage2.rb

@@ -124,14 +124,15 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.select_all <<~SQL
           SELECT o.person_id, o.value_coded
           FROM obs #{current_partition} o
-          LEFT JOIN obs #{current_partition} a ON a.obs_id = o.obs_id and a.obs_datetime > o.obs_datetime and a.concept_id in (#{pregnant_concepts.to_sql}) and a.voided = 0
+          LEFT JOIN obs #{current_partition} a ON a.person_id = o.person_id AND a.obs_datetime > o.obs_datetime AND a.concept_id IN (#{pregnant_concepts.to_sql}) AND a.voided = 0
           AND a.obs_datetime >= DATE(#{ActiveRecord::Base.connection.quote(start_date)}) AND a.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
           WHERE a.obs_id is null
-            and o.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
+            AND o.obs_datetime >= DATE(#{ActiveRecord::Base.connection.quote(start_date)})
+            AND o.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
             AND o.voided = 0
             AND o.concept_id in (#{pregnant_concepts.to_sql})
-            AND o.value_coded IN (#{yes_concepts.join(',')})
             AND o.person_id IN (#{patient_list.join(',')})
+            AND o.value_coded IN (#{yes_concepts.join(',')})
           GROUP BY o.person_id
         SQL
       end
@@ -140,14 +141,15 @@ module MalawiHivProgramReports
         ActiveRecord::Base.connection.select_all <<~SQL
           SELECT o.person_id, o.value_coded
           FROM obs #{current_partition} o
-          LEFT JOIN obs #{current_partition} a ON a.obs_id = o.obs_id and a.obs_datetime > o.obs_datetime and a.concept_id in (#{breast_feeding_concepts.to_sql}) and a.voided = 0
+          LEFT JOIN obs #{current_partition} a ON a.person_id = o.person_id AND a.obs_datetime > o.obs_datetime AND a.concept_id IN (#{breast_feeding_concepts.to_sql}) AND a.voided = 0
           AND a.obs_datetime >= DATE(#{ActiveRecord::Base.connection.quote(start_date)}) AND a.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
           WHERE a.obs_id is null
-            and o.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
+            AND o.obs_datetime >= DATE(#{ActiveRecord::Base.connection.quote(start_date)})
+            AND o.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
             AND o.voided = 0
             AND o.concept_id IN (#{breast_feeding_concepts.to_sql})
-            AND o.value_coded IN (#{yes_concepts.join(',')})
             AND o.person_id IN (#{patient_list.join(',')})
+            AND o.value_coded IN (#{yes_concepts.join(',')})
           GROUP BY o.person_id
         SQL
       end

data/lib/malawi_hiv_program_reports/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module MalawiHivProgramReports
-  VERSION = '1.1.3'
+  VERSION = '1.1.5'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: malawi_hiv_program_reports
 version: !ruby/object:Gem::Version
-  version: 1.1.3
+  version: 1.1.5
 platform: ruby
 authors:
 - Roy Chanunkha
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-06-20 00:00:00.000000000 Z
+date: 2024-06-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails