malawi_hiv_program_reports 1.0.25 → 1.0.26

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Files changed (8) hide show
  1. checksums.yaml +4 -4
  2. data/app/services/malawi_hiv_program_reports/moh/cumulative_cohort.rb +62 -55
  3. data/app/services/malawi_hiv_program_reports/moh/cumulative_outcome.rb +255 -212
  4. data/app/services/malawi_hiv_program_reports/pepfar/tx_ml.rb +55 -110
  5. data/app/services/malawi_hiv_program_reports/pepfar/tx_new.rb +58 -59
  6. data/app/services/malawi_hiv_program_reports/pepfar/tx_rtt.rb +42 -160
  7. data/lib/malawi_hiv_program_reports/version.rb +1 -1
  8. metadata +2 -2
data/app/services/malawi_hiv_program_reports/moh/cumulative_outcome.rb CHANGED
@@ -4,22 +4,39 @@ module MalawiHivProgramReports
4
4
  module Moh
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5
  # This is the Cumulative Cohort Builder class
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  # rubocop:disable Metrics/ClassLength
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+ # rubocop:disable Metrics/MethodLength
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  class CumulativeOutcome
8
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  include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
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- attr_reader :end_date, :definition, :rebuild, :location
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+ attr_reader :end_date, :definition, :rebuild, :start_date, :prev_date, :location
10
11
 
11
12
  def initialize(end_date:, definition: 'moh', **kwargs)
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+ start_date = kwargs[:start_date] || (end_date.to_date - 2.months).beginning_of_month
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  @end_date = ActiveRecord::Base.connection.quote(end_date.to_date)
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+ @start_date = ActiveRecord::Base.connection.quote(start_date.to_date)
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+ @prev_date = ActiveRecord::Base.connection.quote((start_date.to_date - 3.months).to_date)
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  @definition = definition
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  @rebuild = kwargs[:rebuild]
15
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  @location = kwargs[:location]
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+ Rails.logger.info "Definition: #{definition}. Rebuild: #{@rebuild}. Location: #{@location}. Start date: #{@start_date}. End date: #{@end_date}. Previous date: #{@prev_date}."
16
21
  end
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22
 
18
23
  def find_report
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  prepare_tables
20
- clear_tables if rebuild
21
- update_steps unless rebuild
22
- process_data
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+ [false, true].each do |start|
26
+ clear_tables(start:) if rebuild
27
+ update_steps(start:, portion: false) unless rebuild
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+ process_data(start:)
29
+ end
30
+ end
31
+
32
+ def update_outcomes_by_definition
33
+ prepare_tables
34
+ [false, true].each do |start|
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+ update_steps(start: start, portion: true)
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+ load_patients_on_treatment(start:)
37
+ load_without_clinical_contact(start:)
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+ load_defaulters(start:)
39
+ end
23
40
  end
24
41
 
25
42
  private
@@ -45,49 +62,67 @@ module MalawiHivProgramReports
45
62
  # Data Management Region
46
63
  # ===================================
47
64
  # rubocop:disable Metrics/MethodLength
48
- def process_data
49
- denormalize
65
+ def process_data(start: false)
66
+ denormalize(start:)
50
67
  # HIC SUNT DRACONIS: The order of the operations below matters,
51
68
  # do not change it unless you know what you are doing!!!
52
- load_patients_who_died
53
- load_patients_who_stopped_treatment
54
- load_patients_without_drug_orders
55
- load_patients_on_treatment
56
- load_without_clinical_contact
57
- load_defaulters
58
- end
59
-
60
- def denormalize
61
- load_max_drug_orders
62
- load_patient_current_medication
63
- update_patient_current_medication
64
- load_min_auto_expire_date
65
- load_max_patient_state
66
- load_patient_current_state
67
- update_patient_current_state
68
- end
69
-
70
- def load_max_drug_orders
71
- ActiveRecord::Base.connection.execute <<~SQL
72
- INSERT INTO cdr_temp_max_drug_orders PARTITION (p#{location})
73
- SELECT o.patient_id, o.site_id, MAX(o.start_date) AS start_date
74
- FROM orders o
75
- INNER JOIN cdr_temp_cohort_members tesd ON tesd.patient_id = o.patient_id AND tesd.site_id = o.site_id
76
- INNER JOIN drug_order ON drug_order.order_id = o.order_id
69
+ load_patients_who_died(start:)
70
+ load_patients_who_stopped_treatment(start:)
71
+ load_patients_without_drug_orders(start:)
72
+ load_patients_on_treatment(start:)
73
+ load_without_clinical_contact(start:)
74
+ load_defaulters(start:)
75
+ end
76
+
77
+ def denormalize(start: false)
78
+ load_max_drug_orders(start:)
79
+ update_max_drug_orders(start:)
80
+ load_patient_current_medication(start:)
81
+ update_patient_current_medication(start:)
82
+ load_min_auto_expire_date(start:)
83
+ load_max_patient_state(start:)
84
+ load_patient_current_state(start:)
85
+ update_patient_current_state(start:)
86
+ end
87
+
88
+ def load_max_drug_orders(start: false)
89
+ ActiveRecord::Base.connection.execute <<~SQL
90
+ INSERT INTO cdr_temp_max_drug_orders#{start ? '_start' : ''} PARTITION (p#{location})
91
+ SELECT o.patient_id, o.site_id, MAX(o.start_date) AS start_date, NUll
92
+ FROM orders PARTITION (p#{location}) AS o
93
+ INNER JOIN cdr_temp_cohort_members PARTITION (p#{location}) AS tesd ON tesd.patient_id = o.patient_id AND tesd.site_id = o.site_id
94
+ INNER JOIN drug_order PARTITION (p#{location}) ON drug_order.order_id = o.order_id
77
95
  AND drug_order.site_id = o.site_id AND drug_order.quantity > 0
78
96
  AND drug_order.drug_inventory_id IN (#{arv_drug})
79
97
  WHERE o.order_type_id = 1 -- drug order
80
- AND o.start_date < (DATE(#{end_date}) + INTERVAL 1 DAY)
81
- AND o.voided = 0 AND o.site_id = #{location}
82
- GROUP BY o.patient_id, o.site_id
83
- ON DUPLICATE KEY UPDATE start_date = VALUES(start_date)
98
+ AND o.start_date < (DATE(#{start ? start_date : end_date }) + INTERVAL 1 DAY)
99
+ AND o.voided = 0
100
+ GROUP BY o.patient_id
101
+ ON DUPLICATE KEY UPDATE start_date = VALUES(start_date), min_order_date = VALUES(min_order_date)
102
+ SQL
103
+ end
104
+
105
+ def update_max_drug_orders(start: false)
106
+ ActiveRecord::Base.connection.execute <<~SQL
107
+ INSERT INTO cdr_temp_max_drug_orders#{start ? '_start' : ''} PARTITION (p#{location})
108
+ SELECT o.patient_id, #{location}, MAX(o.start_date) AS start_date, MIN(o.start_date) AS min_order_date
109
+ FROM orders PARTITION (p#{location}) AS o
110
+ INNER JOIN cdr_temp_cohort_members PARTITION (p#{location}) AS tesd ON tesd.patient_id = o.patient_id
111
+ INNER JOIN drug_order PARTITION (p#{location}) ON drug_order.order_id = o.order_id AND drug_order.quantity > 0
112
+ AND drug_order.drug_inventory_id IN (#{arv_drug})
113
+ WHERE o.order_type_id = 1 -- drug order
114
+ AND o.start_date < (DATE(#{start ? start_date : end_date }) + INTERVAL 1 DAY)
115
+ AND o.start_date >= (DATE(#{start ? prev_date : start_date }) + INTERVAL 1 DAY)
116
+ AND o.voided = 0
117
+ GROUP BY o.patient_id
118
+ ON DUPLICATE KEY UPDATE start_date = VALUES(start_date), min_order_date = VALUES(min_order_date)
84
119
  SQL
85
120
  end
86
121
 
87
- def load_patient_current_medication
122
+ def load_patient_current_medication(start: false)
88
123
  ActiveRecord::Base.connection.execute <<~SQL
89
- INSERT INTO cdr_temp_current_medication PARTITION (p#{location})
90
- SELECT mdo.patient_id, mdo.site_id, d.concept_id, do.drug_inventory_id drug_id,
124
+ INSERT INTO cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location})
125
+ SELECT mdo.patient_id, #{location}, d.concept_id, do.drug_inventory_id drug_id,
91
126
  CASE
92
127
  WHEN do.equivalent_daily_dose IS NULL THEN 1
93
128
  WHEN do.equivalent_daily_dose = 0 THEN 1
@@ -96,143 +131,135 @@ module MalawiHivProgramReports
96
131
  END daily_dose,
97
132
  SUM(do.quantity) quantity,
98
133
  DATE(mdo.start_date) start_date, null, null, null, null
99
- FROM cdr_temp_max_drug_orders mdo
100
- INNER JOIN orders o ON o.patient_id = mdo.patient_id AND o.site_id = mdo.site_id AND o.order_type_id = 1 AND DATE(o.start_date) = DATE(mdo.start_date) AND o.voided = 0
101
- INNER JOIN drug_order do ON do.order_id = o.order_id AND do.site_id = o.site_id AND do.quantity > 0 AND do.drug_inventory_id IN (#{arv_drug})
134
+ FROM cdr_temp_max_drug_orders#{start ? '_start' : ''} PARTITION (p#{location}) AS mdo
135
+ INNER JOIN orders PARTITION (p#{location}) AS o ON o.patient_id = mdo.patient_id AND o.order_type_id = 1 AND DATE(o.start_date) = DATE(mdo.start_date) AND o.voided = 0
136
+ INNER JOIN drug_order PARTITION (p#{location}) AS do ON do.order_id = o.order_id AND do.quantity > 0 AND do.drug_inventory_id IN (#{arv_drug})
102
137
  INNER JOIN drug d ON d.drug_id = do.drug_inventory_id
103
- WHERE mdo.site_id = #{location}
104
138
  GROUP BY mdo.patient_id, do.drug_inventory_id HAVING quantity < 6000
105
139
  ON DUPLICATE KEY UPDATE concept_id = VALUES(concept_id), daily_dose = VALUES(daily_dose), quantity=VALUES(quantity), start_date = VALUES(start_date), pill_count = VALUES(pill_count), expiry_date = VALUES(expiry_date), pepfar_defaulter_date = VALUES(pepfar_defaulter_date), moh_defaulter_date = VALUES(moh_defaulter_date)
106
140
  SQL
107
141
  end
108
142
 
109
- def update_patient_current_medication
143
+ def update_patient_current_medication(start: false)
110
144
  ActiveRecord::Base.connection.execute <<~SQL
111
- INSERT INTO cdr_temp_current_medication PARTITION (p#{location})
112
- SELECT cm.patient_id, cm.site_id, cm.concept_id, cm.drug_id, cm.daily_dose, cm.quantity, cm.start_date,
145
+ INSERT INTO cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location})
146
+ SELECT cm.patient_id, #{location}, cm.concept_id, cm.drug_id, cm.daily_dose, cm.quantity, cm.start_date,
113
147
  COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0) AS pill_count,
114
- DATE_ADD(DATE_SUB(cm.start_date, INTERVAL 1 DAY), INTERVAL (cm.quantity + COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0)) / cm.daily_dose DAY),
115
- DATE_ADD(DATE_ADD(DATE_SUB(cm.start_date, INTERVAL 1 DAY), INTERVAL (cm.quantity + COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0)) / cm.daily_dose DAY), INTERVAL 30 DAY),
116
- DATE_ADD(DATE_ADD(DATE_SUB(cm.start_date, INTERVAL 1 DAY), INTERVAL (cm.quantity + COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0)) / cm.daily_dose DAY), INTERVAL 60 DAY)
117
- FROM cdr_temp_current_medication cm
148
+ DATE_ADD(cm.start_date, INTERVAL (cm.quantity + COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0)) / cm.daily_dose DAY),
149
+ DATE_ADD(DATE_ADD(cm.start_date, INTERVAL (cm.quantity + COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0)) / cm.daily_dose DAY), INTERVAL 30 DAY),
150
+ DATE_ADD(DATE_ADD(cm.start_date, INTERVAL (cm.quantity + COALESCE(first_ob.quantity, 0) + COALESCE(SUM(second_ob.value_numeric),0) + COALESCE(SUM(third_ob.value_numeric),0)) / cm.daily_dose DAY), INTERVAL 60 DAY)
151
+ FROM cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location}) AS cm
118
152
  LEFT JOIN (
119
- SELECT ob.person_id,ob.site_id, cm.drug_id,
120
- SUM(ob.value_numeric) + SUM(CASE
121
- WHEN ob.value_text is null then 0
122
- WHEN ob.value_text REGEXP '^[0-9]+(.[0-9]+)?$' then ob.value_text
123
- ELSE 0
124
- END) quantity
125
- FROM obs ob
126
- INNER JOIN cdr_temp_current_medication cm ON cm.patient_id = ob.person_id AND cm.site_id = ob.site_id AND cm.start_date = DATE(ob.obs_datetime)
127
- INNER JOIN orders o ON o.order_id = ob.order_id AND o.site_id = ob.site_id AND o.voided = 0
128
- INNER JOIN drug_order do ON do.order_id = o.order_id AND do.site_id = o.site_id AND do.drug_inventory_id = cm.drug_id
129
- WHERE ob.concept_id = 2540 AND ob.voided = 0 AND ob.site_id = #{location}
130
- GROUP BY ob.person_id, cm.drug_id
131
- ) first_ob ON first_ob.person_id = cm.patient_id AND first_ob.site_id = cm.site_id AND first_ob.drug_id = cm.drug_id
132
- LEFT JOIN obs second_ob ON second_ob.person_id = cm.patient_id AND second_ob.site_id = cm.site_id AND second_ob.concept_id = cm.concept_id AND DATE(second_ob.obs_datetime) = cm.start_date AND second_ob.voided = 0
133
- LEFT JOIN obs third_ob ON third_ob.person_id = cm.patient_id AND third_ob.site_id = cm.site_id AND third_ob.concept_id = 2540 AND third_ob.value_drug = cm.drug_id AND third_ob.voided = 0 AND DATE(third_ob.obs_datetime) = cm.start_date
134
- WHERE cm.site_id = #{location}
153
+ SELECT ob.person_id, #{location}, cm.drug_id,
154
+ SUM(ob.value_numeric) + SUM(CASE
155
+ WHEN ob.value_text is null then 0
156
+ WHEN ob.value_text REGEXP '^[0-9]+(.[0-9]+)?$' then ob.value_text
157
+ ELSE 0
158
+ END) quantity
159
+ FROM obs PARTITION (p#{location}) AS ob
160
+ INNER JOIN cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location}) cm ON cm.patient_id = ob.person_id AND cm.start_date = DATE(ob.obs_datetime)
161
+ INNER JOIN orders PARTITION (p#{location}) o ON o.order_id = ob.order_id AND o.voided = 0
162
+ INNER JOIN drug_order PARTITION (p#{location}) AS do ON do.order_id = o.order_id AND do.drug_inventory_id = cm.drug_id
163
+ WHERE ob.concept_id = 2540 AND ob.voided = 0
164
+ GROUP BY ob.person_id, cm.drug_id
165
+ ) first_ob ON first_ob.person_id = cm.patient_id AND first_ob.drug_id = cm.drug_id
166
+ LEFT JOIN obs PARTITION (p#{location}) As second_ob ON second_ob.person_id = cm.patient_id AND second_ob.concept_id = cm.concept_id AND DATE(second_ob.obs_datetime) = cm.start_date AND second_ob.voided = 0
167
+ LEFT JOIN obs PARTITION (p#{location}) AS third_ob ON third_ob.person_id = cm.patient_id AND third_ob.concept_id = 2540 AND third_ob.value_drug = cm.drug_id AND third_ob.voided = 0 AND DATE(third_ob.obs_datetime) = cm.start_date
135
168
  GROUP BY cm.patient_id, cm.drug_id
136
169
  ON DUPLICATE KEY UPDATE pill_count = VALUES(pill_count), expiry_date = VALUES(expiry_date), pepfar_defaulter_date = VALUES(pepfar_defaulter_date), moh_defaulter_date = VALUES(moh_defaulter_date);
137
170
  SQL
138
171
  end
139
172
 
140
- def load_min_auto_expire_date
173
+ def load_min_auto_expire_date(start: false)
141
174
  ActiveRecord::Base.connection.execute <<~SQL
142
- INSERT INTO cdr_temp_min_auto_expire_date PARTITION (p#{location})
143
- SELECT cm.patient_id, cm.site_id, MIN(cm.start_date), MIN(cm.expiry_date), MIN(cm.pepfar_defaulter_date), MIN(cm.moh_defaulter_date)
144
- FROM cdr_temp_current_medication cm
145
- WHERE cm.site_id = #{location}
175
+ INSERT INTO cdr_temp_min_auto_expire_date#{start ? '_start' : ''} PARTITION (p#{location})
176
+ SELECT cm.patient_id, #{location}, MIN(cm.start_date), MIN(cm.expiry_date), MIN(cm.pepfar_defaulter_date), MIN(cm.moh_defaulter_date)
177
+ FROM cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location}) AS cm
146
178
  GROUP BY cm.patient_id
147
179
  ON DUPLICATE KEY UPDATE start_date = VALUES(start_date), auto_expire_date = VALUES(auto_expire_date), pepfar_defaulter_date = VALUES(pepfar_defaulter_date), moh_defaulter_date = VALUES(moh_defaulter_date)
148
180
  SQL
149
181
  end
150
182
 
151
- def load_max_patient_state
183
+ def load_max_patient_state(start: false)
152
184
  ActiveRecord::Base.connection.execute <<~SQL
153
- INSERT INTO cdr_temp_max_patient_state PARTITION (p#{location})
154
- SELECT pp.patient_id, pp.site_id, MAX(ps.start_date) start_date
155
- FROM patient_state ps
156
- INNER JOIN patient_program pp ON pp.patient_program_id = ps.patient_program_id AND pp.site_id = ps.site_id AND pp.program_id = 1 AND pp.voided = 0
185
+ INSERT INTO cdr_temp_max_patient_state#{start ? '_start' : ''} PARTITION (p#{location})
186
+ SELECT pp.patient_id, #{location}, MAX(ps.start_date) start_date
187
+ FROM patient_state PARTITION (p#{location}) AS ps
188
+ 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
157
189
  WHERE ps.start_date < DATE(#{end_date}) + INTERVAL 1 DAY
158
- AND ps.voided = 0 AND ps.site_id = #{location} AND pp.patient_id IN (SELECT patient_id FROM temp_earliest_start_date WHERE site_id = #{location})
159
- GROUP BY pp.patient_id, pp.site_id
190
+ AND ps.voided = 0 AND pp.patient_id IN (SELECT patient_id FROM cdr_temp_cohort_members PARTITION (p#{location}))
191
+ GROUP BY pp.patient_id
160
192
  HAVING start_date IS NOT NULL
161
193
  ON DUPLICATE KEY UPDATE start_date = VALUES(start_date)
162
194
  SQL
163
195
  end
164
196
 
165
- def load_patient_current_state
197
+ def load_patient_current_state(start: false)
166
198
  ActiveRecord::Base.connection.execute <<~SQL
167
- INSERT INTO cdr_temp_current_state PARTITION (p#{location})
168
- SELECT mps.patient_id, mps.site_id, cn.name AS cum_outcome, ps.start_date as outcome_date, ps.state, count(DISTINCT(ps.state)) outcomes, MAX(ps.patient_state_id) patient_state_id
169
- FROM cdr_temp_max_patient_state mps
170
- INNER JOIN patient_program pp ON pp.patient_id = mps.patient_id AND pp.site_id = mps.site_id AND pp.program_id = 1 AND pp.voided = 0
171
- INNER JOIN patient_state ps ON ps.patient_program_id = pp.patient_program_id AND ps.site_id = pp.site_id AND ps.start_date = mps.start_date AND ps.voided = 0
199
+ INSERT INTO cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location})
200
+ SELECT mps.patient_id, #{location}, cn.name AS cum_outcome, ps.start_date as outcome_date, ps.state, count(DISTINCT(ps.state)) outcomes, MAX(ps.patient_state_id) patient_state_id
201
+ FROM cdr_temp_max_patient_state#{start ? '_start' : ''} PARTITION (p#{location}) AS mps
202
+ INNER JOIN patient_program PARTITION (p#{location}) AS pp ON pp.patient_id = mps.patient_id AND pp.program_id = 1 AND pp.voided = 0
203
+ INNER JOIN patient_state PARTITION (p#{location}) AS ps ON ps.patient_program_id = pp.patient_program_id AND ps.start_date = mps.start_date AND ps.voided = 0
172
204
  AND (ps.end_date IS NULL OR ps.end_date > DATE(#{end_date}))
173
205
  INNER JOIN program_workflow_state pws ON pws.program_workflow_state_id = ps.state AND pws.retired = 0
174
206
  INNER JOIN concept_name cn ON cn.concept_id = pws.concept_id AND cn.concept_name_type = 'FULLY_SPECIFIED' AND cn.voided = 0
175
- LEFT JOIN patient_state ps2 ON ps.patient_program_id = ps2.patient_program_id AND ps2.site_id = ps.site_id AND ps.start_date = ps2.start_date AND ps.date_created < ps2.date_created AND ps2.voided = 0
176
- WHERE ps2.patient_program_id IS NULL AND ps.voided = 0 AND mps.site_id = #{location}
207
+ LEFT JOIN patient_state PARTITION (p#{location}) AS ps2 ON ps.patient_program_id = ps2.patient_program_id AND ps.start_date = ps2.start_date AND ps.date_created < ps2.date_created AND ps2.voided = 0
208
+ WHERE ps2.patient_program_id IS NULL AND ps.voided = 0
177
209
  GROUP BY mps.patient_id
178
210
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), state = VALUES(state), outcomes = VALUES(outcomes)
179
211
  SQL
180
212
  end
181
213
 
182
- def update_patient_current_state
214
+ def update_patient_current_state(start: false)
183
215
  ActiveRecord::Base.connection.execute <<~SQL
184
- INSERT INTO cdr_temp_current_state
185
- SELECT cs.patient_id, cs.site_id, cn.name as cum_outcome, ps.start_date as outcome_date, ps.state, 1, cs.patient_state_id
186
- FROM patient_state ps
187
- INNER JOIN cdr_temp_current_state cs ON cs.patient_state_id = ps.patient_state_id AND cs.site_id = ps.site_id
216
+ INSERT INTO cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location})
217
+ SELECT cs.patient_id, #{location}, cn.name as cum_outcome, ps.start_date as outcome_date, ps.state, 1, cs.patient_state_id
218
+ FROM patient_state PARTITION (p#{location}) ps
219
+ INNER JOIN cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location}) AS cs ON cs.patient_state_id = ps.patient_state_id AND cs.site_id = ps.site_id
188
220
  INNER JOIN program_workflow_state pws ON pws.program_workflow_state_id = ps.state AND pws.retired = 0
189
221
  INNER JOIN concept_name cn ON cn.concept_id = pws.concept_id AND cn.concept_name_type = 'FULLY_SPECIFIED' AND cn.voided = 0
190
- WHERE ps.voided = 0 AND cs.outcomes > 1 AND cs.site_id = #{location}
222
+ WHERE ps.voided = 0 AND cs.outcomes > 1
191
223
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), state = VALUES(state), outcomes = VALUES(outcomes), patient_state_id = VALUES(patient_state_id)
192
224
  SQL
193
225
  end
194
226
 
195
227
  # Loads all patiens with an outcome of died as of given date
196
228
  # into the temp_patient_outcomes table.
197
- def load_patients_who_died
229
+ def load_patients_who_died(start: false)
198
230
  ActiveRecord::Base.connection.execute <<~SQL
199
- INSERT INTO cdr_temp_patient_outcomes PARTITION (p#{location})
200
- SELECT patients.patient_id, 'Patient died', patient_state.start_date, patients.site_id, 1
201
- FROM cdr_temp_cohort_members AS patients
202
- INNER JOIN patient_program
231
+ INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
232
+ SELECT patients.patient_id, 'Patient died', patient_state.start_date, #{location}, 1
233
+ FROM cdr_temp_cohort_members PARTITION (p#{location}) AS patients
234
+ INNER JOIN patient_program PARTITION (p#{location})
203
235
  ON patient_program.patient_id = patients.patient_id
204
- AND patient_program.site_id = patients.site_id
205
236
  AND patient_program.program_id = 1
206
237
  AND patient_program.voided = 0
207
- INNER JOIN patient_state
238
+ INNER JOIN patient_state PARTITION (p#{location})
208
239
  ON patient_state.patient_program_id = patient_program.patient_program_id
209
- AND patient_state.site_id = patient_program.site_id
210
240
  AND patient_state.state = (#{program_states('Patient died').limit(1).to_sql})
211
241
  AND patient_state.start_date < DATE(#{end_date}) + INTERVAL 1 DAY
212
242
  AND patient_state.voided = 0
213
- WHERE patients.date_enrolled <= DATE(#{end_date}) AND patients.site_id = #{location}
243
+ WHERE patients.date_enrolled <= DATE(#{end_date})
214
244
  AND patient_state.date_created = (
215
245
  SELECT MAX(date_created)
216
- FROM patient_state ps
217
- WHERE ps.patient_program_id = patient_state.patient_program_id AND ps.site_id = patient_state.site_id
246
+ FROM patient_state PARTITION (p#{location}) ps
247
+ WHERE ps.patient_program_id = patient_state.patient_program_id
218
248
  AND ps.state = patient_state.state AND ps.voided = 0 AND ps.start_date <= #{end_date})
219
- GROUP BY patients.patient_id, patients.site_id
249
+ GROUP BY patients.patient_id
220
250
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
221
251
  SQL
222
252
  end
223
253
 
224
254
  # Loads all patients with an outcome of transferred out or
225
255
  # treatment stopped into temp_patient_outcomes table.
226
- def load_patients_who_stopped_treatment
227
- ActiveRecord::Base.connection.execute <<~SQL
228
- INSERT INTO cdr_temp_patient_outcomes PARTITION (p#{location})
229
- SELECT patients.patient_id,
230
- patients.cum_outcome,
231
- patients.outcome_date, patients.site_id, 2
232
- FROM cdr_temp_current_state AS patients
233
- WHERE (patients.patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes PARTITION (p#{location}) WHERE step = 1)
256
+ def load_patients_who_stopped_treatment(start: false)
257
+ ActiveRecord::Base.connection.execute <<~SQL
258
+ INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
259
+ SELECT patients.patient_id,patients.cum_outcome,patients.outcome_date, #{location}, 2
260
+ FROM cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location}) AS patients
261
+ WHERE (patients.patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location}) WHERE step = 1)
234
262
  AND patients.outcomes = 1
235
- AND patients.site_id = #{location}
236
263
  AND patients.state IN (
237
264
  SELECT pws.program_workflow_state_id state
238
265
  FROM program_workflow pw
@@ -247,53 +274,51 @@ module MalawiHivProgramReports
247
274
 
248
275
  # Load all patients without drug orders or have drug orders
249
276
  # without a quantity.
250
- def load_patients_without_drug_orders
251
- ActiveRecord::Base.connection.execute <<~SQL
252
- INSERT INTO cdr_temp_patient_outcomes PARTITION (p#{location})
253
- SELECT patients.patient_id, 'Unknown', NULL, patients.site_id, 3
254
- FROM cdr_temp_cohort_members AS patients
255
- WHERE date_enrolled <= #{end_date} AND site_id = #{location}
256
- AND (patient_id, site_id) NOT IN (SELECT patient_id, site_id FROM cdr_temp_patient_outcomes PARTITION (p#{location}) WHERE step IN (1, 2, 3, 4))
257
- AND (patient_id, site_id) NOT IN (SELECT patient_id, site_id FROM cdr_temp_max_drug_orders PARTITION (p#{location}))
277
+ def load_patients_without_drug_orders(start: false)
278
+ ActiveRecord::Base.connection.execute <<~SQL
279
+ INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
280
+ SELECT patients.patient_id, 'Unknown', NULL, #{location}, 3
281
+ FROM cdr_temp_cohort_members PARTITION (p#{location}) AS patients
282
+ WHERE date_enrolled <= #{end_date}
283
+ 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))
284
+ AND (patient_id) NOT IN (SELECT patient_id FROM cdr_temp_max_drug_orders#{start ? '_start' : ''} PARTITION (p#{location}))
258
285
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
259
286
  SQL
260
287
  end
261
288
 
262
289
  # Loads all patients who are on treatment
263
- def load_patients_on_treatment
264
- ActiveRecord::Base.connection.execute <<~SQL
265
- INSERT INTO cdr_temp_patient_outcomes PARTITION (p#{location})
266
- SELECT patients.patient_id, 'On antiretrovirals', COALESCE(cs.outcome_date, patients.start_date), patients.site_id, 4
267
- FROM cdr_temp_min_auto_expire_date AS patients
268
- LEFT JOIN cdr_temp_current_state AS cs ON cs.patient_id = patients.patient_id AND cs.site_id = patients.site_id
269
- WHERE patients.#{@definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} > #{end_date}
270
- AND (patients.patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes PARTITION (p#{location}) WHERE step IN (1, 2, 3))
271
- AND patients.site_id = #{location}
290
+ def load_patients_on_treatment(start: false)
291
+ ActiveRecord::Base.connection.execute <<~SQL
292
+ INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
293
+ SELECT patients.patient_id, 'On antiretrovirals', COALESCE(cs.outcome_date, patients.start_date), #{location}, 4
294
+ FROM cdr_temp_min_auto_expire_date#{start ? '_start' : ''} PARTITION (p#{location}) AS patients
295
+ 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
296
+ WHERE patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} > #{end_date}
297
+ 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))
272
298
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
273
299
  SQL
274
300
  end
275
301
 
276
- def load_without_clinical_contact
302
+ def load_without_clinical_contact(start: false)
277
303
  ActiveRecord::Base.connection.execute <<~SQL
278
- INSERT INTO cdr_temp_patient_outcomes PARTITION (p#{location})
279
- SELECT patients.patient_id, 'Defaulted', patients.#{@definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'}, patients.site_id, 5
280
- FROM cdr_temp_current_medication AS patients
281
- LEFT JOIN cdr_temp_current_state AS cs ON cs.patient_id = patients.patient_id AND cs.site_id = patients.site_id#{' '}
282
- WHERE patients.#{@definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} <= #{end_date}
283
- AND (patients.patient_id) NOT IN (SELECT patient_id FROM cdr_temp_patient_outcomes PARTITION (p#{location}) WHERE step IN (1, 2, 3, 4))
284
- AND patients.site_id = #{location}
304
+ INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
305
+ SELECT patients.patient_id, 'Defaulted', patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'},#{location}, 5
306
+ FROM cdr_temp_current_medication#{start ? '_start' : ''} PARTITION (p#{location}) AS patients
307
+ LEFT JOIN cdr_temp_current_state#{start ? '_start' : ''} PARTITION (p#{location}) AS cs ON cs.patient_id = patients.patient_id
308
+ WHERE patients.#{definition == 'pepfar' ? 'pepfar_defaulter_date' : 'moh_defaulter_date'} <= #{end_date}
309
+ 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))
285
310
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
286
311
  SQL
287
312
  end
288
313
 
289
314
  # Load defaulters
290
- def load_defaulters
315
+ def load_defaulters(start: false)
291
316
  ActiveRecord::Base.connection.execute <<~SQL
292
- INSERT INTO cdr_temp_patient_outcomes PARTITION (p#{location})
293
- SELECT patient_id, #{patient_outcome_function('patient_id', 'site_id')}, NULL, site_id, 6
294
- FROM cdr_temp_cohort_members
295
- WHERE date_enrolled <= #{end_date} AND site_id = #{location}
296
- AND (patient_id, site_id) NOT IN (SELECT patient_id, site_id FROM cdr_temp_patient_outcomes PARTITION (p#{location}) WHERE step IN (1, 2, 3, 4, 5))
317
+ INSERT INTO cdr_temp_patient_outcomes#{start ? '_start' : ''} PARTITION (p#{location})
318
+ SELECT patient_id, #{patient_outcome_function('patient_id', 'site_id')}, NULL, #{location}, 6
319
+ FROM cdr_temp_cohort_members PARTITION (p#{location})
320
+ WHERE date_enrolled <= #{end_date}
321
+ 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))
297
322
  ON DUPLICATE KEY UPDATE cum_outcome = VALUES(cum_outcome), outcome_date = VALUES(outcome_date), step = VALUES(step)
298
323
  SQL
299
324
  end
@@ -315,14 +340,18 @@ module MalawiHivProgramReports
315
340
  # Table Management Region
316
341
  # ===================================
317
342
  def prepare_tables
318
- create_outcome_table unless check_if_table_exists('cdr_temp_patient_outcomes')
319
- create_tmp_max_drug_orders_table unless check_if_table_exists('cdr_temp_max_drug_orders')
320
- create_tmp_min_auto_expire_date unless check_if_table_exists('cdr_temp_min_auto_expire_date')
321
- drop_tmp_min_auto_expirte_date unless count_table_columns('cdr_temp_min_auto_expire_date') == 6
322
- create_cdr_temp_max_patient_state unless check_if_table_exists('cdr_temp_max_patient_state')
323
- create_temp_current_state unless check_if_table_exists('cdr_temp_current_state')
324
- drop_temp_current_state unless count_table_columns('cdr_temp_current_state') == 7
325
- create_temp_current_medication unless check_if_table_exists('cdr_temp_current_medication')
343
+ [false, true].each do |start|
344
+ create_outcome_table(start:) unless check_if_table_exists("cdr_temp_patient_outcomes#{start ? '_start' : ''}")
345
+ drop_temp_patient_outcome_table(start:) unless count_table_columns("cdr_temp_patient_outcomes#{start ? '_start' : ''}") == 5
346
+ create_tmp_max_drug_orders_table(start:) unless check_if_table_exists("cdr_temp_max_drug_orders#{start ? '_start' : ''}")
347
+ drop_temp_max_drug_orders_table(start:) unless count_table_columns("cdr_temp_max_drug_orders#{start ? '_start' : ''}") == 4
348
+ create_tmp_min_auto_expire_date(start:) unless check_if_table_exists("cdr_temp_min_auto_expire_date#{start ? '_start' : ''}")
349
+ drop_tmp_min_auto_expirte_date(start:) unless count_table_columns("cdr_temp_min_auto_expire_date#{start ? '_start' : ''}") == 6
350
+ create_cdr_temp_max_patient_state(start:) unless check_if_table_exists("cdr_temp_max_patient_state#{start ? '_start' : ''}")
351
+ create_temp_current_state(start:) unless check_if_table_exists("cdr_temp_current_state#{start ? '_start' : ''}")
352
+ drop_temp_current_state(start:) unless count_table_columns("cdr_temp_current_state#{start ? '_start' : ''}") == 7
353
+ create_temp_current_medication(start:) unless check_if_table_exists("cdr_temp_current_medication#{start ? '_start' : ''}")
354
+ end
326
355
  end
327
356
 
328
357
  def check_if_table_exists(table_name)
@@ -345,9 +374,9 @@ module MalawiHivProgramReports
345
374
  result['count'].to_i
346
375
  end
347
376
 
348
- def create_outcome_table
377
+ def create_outcome_table(start: false)
349
378
  ActiveRecord::Base.connection.execute <<~SQL
350
- CREATE TABLE IF NOT EXISTS cdr_temp_patient_outcomes (
379
+ CREATE TABLE IF NOT EXISTS cdr_temp_patient_outcomes#{start ? '_start' : ''} (
351
380
  patient_id INT NOT NULL,
352
381
  cum_outcome VARCHAR(120) NOT NULL,
353
382
  outcome_date DATE DEFAULT NULL,
@@ -357,43 +386,56 @@ module MalawiHivProgramReports
357
386
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8
358
387
  PARTITION BY LIST(site_id) (#{partition_by_site})
359
388
  SQL
360
- create_outcome_indexes
389
+ create_outcome_indexes(start:)
361
390
  end
362
391
 
363
- def create_outcome_indexes
392
+ def drop_temp_patient_outcome_table(start: false)
393
+ ActiveRecord::Base.connection.execute <<~SQL
394
+ DROP TABLE IF EXISTS cdr_temp_patient_outcomes#{start ? '_start' : ''}
395
+ SQL
396
+ create_outcome_table(start:)
397
+ end
398
+
399
+ def create_outcome_indexes(start: false)
364
400
  ActiveRecord::Base.connection.execute <<~SQL
365
- CREATE INDEX idx_outcome ON cdr_temp_patient_outcomes (cum_outcome)
401
+ CREATE INDEX idx_outcome#{start ? '_start' : ''} ON cdr_temp_patient_outcomes#{start ? '_start' : ''} (cum_outcome)
366
402
  SQL
367
403
  ActiveRecord::Base.connection.execute <<~SQL
368
- CREATE INDEX idx_out_date ON cdr_temp_patient_outcomes (outcome_date)
404
+ CREATE INDEX idx_out_date#{start ? '_start' : ''} ON cdr_temp_patient_outcomes#{start ? '_start' : ''} (outcome_date)
369
405
  SQL
370
406
  ActiveRecord::Base.connection.execute <<~SQL
371
- CREATE INDEX idx_out_step ON cdr_temp_patient_outcomes (step)
407
+ CREATE INDEX idx_out_step#{start ? '_start' : ''} ON cdr_temp_patient_outcomes#{start ? '_start' : ''} (step)
372
408
  SQL
373
409
  end
374
410
 
375
- def create_tmp_max_drug_orders_table
411
+ def drop_temp_max_drug_orders_table(start: false)
412
+ ActiveRecord::Base.connection.execute("DROP TABLE IF EXISTS cdr_temp_max_drug_orders#{start ? '_start' : ''}")
413
+ create_tmp_max_drug_orders_table(start:)
414
+ end
415
+
416
+ def create_tmp_max_drug_orders_table(start: false)
376
417
  ActiveRecord::Base.connection.execute <<~SQL
377
- CREATE TABLE IF NOT EXISTS cdr_temp_max_drug_orders (
418
+ CREATE TABLE IF NOT EXISTS cdr_temp_max_drug_orders#{start ? '_start' : ''} (
378
419
  patient_id INT NOT NULL,
379
420
  site_id INT NOT NULL,
380
421
  start_date DATETIME DEFAULT NULL,
422
+ min_order_date DATETIME DEFAULT NULL,
381
423
  PRIMARY KEY (patient_id, site_id)
382
424
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8
383
425
  PARTITION BY LIST(site_id) (#{partition_by_site})
384
426
  SQL
385
- create_max_drug_orders_indexes
427
+ create_max_drug_orders_indexes(start:)
386
428
  end
387
429
 
388
- def create_max_drug_orders_indexes
430
+ def create_max_drug_orders_indexes(start: false)
389
431
  ActiveRecord::Base.connection.execute <<~SQL
390
- CREATE INDEX idx_max_orders ON cdr_temp_max_drug_orders (start_date)
432
+ CREATE INDEX idx_max_orders#{start ? '_start' : ''} ON cdr_temp_max_drug_orders#{start ? '_start' : ''} (start_date)
391
433
  SQL
392
434
  end
393
435
 
394
- def create_tmp_min_auto_expire_date
436
+ def create_tmp_min_auto_expire_date(start: false)
395
437
  ActiveRecord::Base.connection.execute <<~SQL
396
- CREATE TABLE IF NOT EXISTS cdr_temp_min_auto_expire_date (
438
+ CREATE TABLE IF NOT EXISTS cdr_temp_min_auto_expire_date#{start ? '_start' : ''} (
397
439
  patient_id INT NOT NULL,
398
440
  site_id INT NOT NULL,
399
441
  start_date DATE DEFAULT NULL,
@@ -404,24 +446,24 @@ module MalawiHivProgramReports
404
446
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8
405
447
  PARTITION BY LIST(site_id) (#{partition_by_site})
406
448
  SQL
407
- create_min_auto_expire_date_indexes
449
+ create_min_auto_expire_date_indexes(start:)
408
450
  end
409
451
 
410
- def create_min_auto_expire_date_indexes
452
+ def create_min_auto_expire_date_indexes(start: false)
411
453
  ActiveRecord::Base.connection.execute <<~SQL
412
- CREATE INDEX idx_min_auto_expire_date ON temp_min_auto_expire_date (auto_expire_date)
454
+ CREATE INDEX idx_min_auto_expire_date#{start ? '_start' : ''} ON temp_min_auto_expire_date#{start ? '_start' : ''} (auto_expire_date)
413
455
  SQL
414
456
  ActiveRecord::Base.connection.execute <<~SQL
415
- CREATE INDEX idx_min_pepfar ON temp_min_auto_expire_date (pepfar_defaulter_date)
457
+ CREATE INDEX idx_min_pepfar#{start ? '_start' : ''} ON temp_min_auto_expire_date#{start ? '_start' : ''} (pepfar_defaulter_date)
416
458
  SQL
417
459
  ActiveRecord::Base.connection.execute <<~SQL
418
- CREATE INDEX idx_min_moh ON temp_min_auto_expire_date (moh_defaulter_date)
460
+ CREATE INDEX idx_min_moh#{start ? '_start' : ''} ON temp_min_auto_expire_date#{start ? '_start' : ''} (moh_defaulter_date)
419
461
  SQL
420
462
  end
421
463
 
422
- def create_cdr_temp_max_patient_state
464
+ def create_cdr_temp_max_patient_state(start: false)
423
465
  ActiveRecord::Base.connection.execute <<~SQL
424
- CREATE TABLE IF NOT EXISTS cdr_temp_max_patient_state (
466
+ CREATE TABLE IF NOT EXISTS cdr_temp_max_patient_state#{start ? '_start' : ''}(
425
467
  patient_id INT NOT NULL,
426
468
  site_id INT NOT NULL,
427
469
  start_date VARCHAR(15) DEFAULT NULL,
@@ -429,18 +471,18 @@ module MalawiHivProgramReports
429
471
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8
430
472
  PARTITION BY LIST(site_id) (#{partition_by_site})
431
473
  SQL
432
- create_max_patient_state_indexes
474
+ create_max_patient_state_indexes(start:)
433
475
  end
434
476
 
435
- def create_max_patient_state_indexes
477
+ def create_max_patient_state_indexes(start: false)
436
478
  ActiveRecord::Base.connection.execute <<~SQL
437
- CREATE INDEX idx_max_patient_state ON cdr_temp_max_patient_state (start_date)
479
+ CREATE INDEX idx_max_patient_state#{start ? '_start' : ''} ON cdr_temp_max_patient_state#{start ? '_start' : ''} (start_date)
438
480
  SQL
439
481
  end
440
482
 
441
- def create_temp_current_state
483
+ def create_temp_current_state(start: false)
442
484
  ActiveRecord::Base.connection.execute <<~SQL
443
- CREATE TABLE IF NOT EXISTS cdr_temp_current_state(
485
+ CREATE TABLE IF NOT EXISTS cdr_temp_current_state#{start ? '_start' : ''}(
444
486
  patient_id INT NOT NULL,
445
487
  site_id INT NOT NULL,
446
488
  cum_outcome VARCHAR(120) NOT NULL,
@@ -452,24 +494,24 @@ module MalawiHivProgramReports
452
494
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8
453
495
  PARTITION BY LIST(site_id) (#{partition_by_site})
454
496
  SQL
455
- create_current_state_index
497
+ create_current_state_index(start:)
456
498
  end
457
499
 
458
- def create_current_state_index
500
+ def create_current_state_index(start: false)
459
501
  ActiveRecord::Base.connection.execute <<~SQL
460
- CREATE INDEX idx_state_name ON cdr_temp_current_state (cum_outcome)
502
+ CREATE INDEX idx_state_name#{start ? '_start' : ''} ON cdr_temp_current_state#{start ? '_start' : ''} (cum_outcome)
461
503
  SQL
462
504
  ActiveRecord::Base.connection.execute <<~SQL
463
- CREATE INDEX idx_state_id ON cdr_temp_current_state (state)
505
+ CREATE INDEX idx_state_id#{start ? '_start' : ''} ON cdr_temp_current_state#{start ? '_start' : ''} (state)
464
506
  SQL
465
507
  ActiveRecord::Base.connection.execute <<~SQL
466
- CREATE INDEX idx_state_count ON cdr_temp_current_state (outcomes)
508
+ CREATE INDEX idx_state_count#{start ? '_start' : ''} ON cdr_temp_current_state#{start ? '_start' : ''} (outcomes)
467
509
  SQL
468
510
  end
469
511
 
470
- def create_temp_current_medication
512
+ def create_temp_current_medication(start: false)
471
513
  ActiveRecord::Base.connection.execute <<~SQL
472
- CREATE TABLE IF NOT EXISTS cdr_temp_current_medication(
514
+ CREATE TABLE IF NOT EXISTS cdr_temp_current_medication#{start ? '_start' : ''}(
473
515
  patient_id INT NOT NULL,
474
516
  site_id INT NOT NULL,
475
517
  concept_id INT NOT NULL,
@@ -485,40 +527,40 @@ module MalawiHivProgramReports
485
527
  ) ENGINE=InnoDB DEFAULT CHARSET=utf8
486
528
  PARTITION BY LIST(site_id) (#{partition_by_site})
487
529
  SQL
488
- craete_tmp_current_med_index
530
+ create_tmp_current_med_index(start:)
489
531
  end
490
532
 
491
- def craete_tmp_current_med_index
533
+ def create_tmp_current_med_index(start: false)
492
534
  ActiveRecord::Base.connection.execute <<~SQL
493
- CREATE INDEX idx_cm_concept ON cdr_temp_current_medication (concept_id)
535
+ CREATE INDEX idx_cm_concept#{start ? '_start' : ''} ON cdr_temp_current_medication#{start ? '_start' : ''} (concept_id)
494
536
  SQL
495
537
  ActiveRecord::Base.connection.execute <<~SQL
496
- CREATE INDEX idx_cm_drug ON cdr_temp_current_medication (drug_id)
538
+ CREATE INDEX idx_cm_drug#{start ? '_start' : ''} ON cdr_temp_current_medication#{start ? '_start' : ''} (drug_id)
497
539
  SQL
498
540
  ActiveRecord::Base.connection.execute <<~SQL
499
- CREATE INDEX idx_cm_date ON cdr_temp_current_medication (start_date)
541
+ CREATE INDEX idx_cm_date#{start ? '_start' : ''} ON cdr_temp_current_medication#{start ? '_start' : ''} (start_date)
500
542
  SQL
501
543
  ActiveRecord::Base.connection.execute <<~SQL
502
- CREATE INDEX idx_cm_pepfar ON cdr_temp_current_medication (pepfar_defaulter_date)
544
+ CREATE INDEX idx_cm_pepfar#{start ? '_start' : ''} ON cdr_temp_current_medication#{start ? '_start' : ''} (pepfar_defaulter_date)
503
545
  SQL
504
546
  ActiveRecord::Base.connection.execute <<~SQL
505
- CREATE INDEX idx_cm_moh ON cdr_temp_current_medication (moh_defaulter_date)
547
+ CREATE INDEX idx_cm_moh#{start ? '_start' : ''} ON cdr_temp_current_medication#{start ? '_start' : ''} (moh_defaulter_date)
506
548
  SQL
507
549
  end
508
550
 
509
- def drop_tmp_min_auto_expirte_date
510
- ActiveRecord::Base.connection.execute 'DROP TABLE cdr_temp_min_auto_expire_date'
511
- create_tmp_min_auto_expire_date
551
+ def drop_tmp_min_auto_expirte_date(start: false)
552
+ ActiveRecord::Base.connection.execute "DROP TABLE cdr_temp_min_auto_expire_date#{start ? '_start' : ''}"
553
+ create_tmp_min_auto_expire_date(start:)
512
554
  end
513
555
 
514
- def drop_temp_current_state
515
- ActiveRecord::Base.connection.execute 'DROP TABLE cdr_temp_current_state'
516
- create_temp_current_state
556
+ def drop_temp_current_state(start: false)
557
+ ActiveRecord::Base.connection.execute "DROP TABLE cdr_temp_current_state#{start ? '_start' : ''}"
558
+ create_temp_current_state(start:)
517
559
  end
518
560
 
519
- def update_steps
561
+ def update_steps(start: false, portion: false)
520
562
  ActiveRecord::Base.connection.execute <<~SQL
521
- UPDATE cdr_temp_patient_outcomes SET step = 0 WHERE step > 0 AND site_id = #{location}
563
+ UPDATE cdr_temp_patient_outcomes#{start ? '_start' : ''} SET step = 0 WHERE step >= #{portion ? 4 : 1 } AND site_id = #{location}
522
564
  SQL
523
565
  end
524
566
 
@@ -526,25 +568,26 @@ module MalawiHivProgramReports
526
568
  @arv_drug ||= ::Drug.arv_drugs.map(&:drug_id).join(',')
527
569
  end
528
570
 
529
- def clear_tables
571
+ def clear_tables(start: false)
530
572
  # we truncate if @locations is empty otherwise we only clean the specifieds
531
573
  if location.empty?
532
- ActiveRecord::Base.connection.execute('TRUNCATE cdr_temp_patient_outcomes')
533
- ActiveRecord::Base.connection.execute('TRUNCATE cdr_temp_max_drug_orders')
534
- ActiveRecord::Base.connection.execute('TRUNCATE cdr_temp_min_auto_expire_date')
535
- ActiveRecord::Base.connection.execute('TRUNCATE cdr_temp_max_patient_state')
536
- ActiveRecord::Base.connection.execute('TRUNCATE cdr_temp_current_state')
537
- ActiveRecord::Base.connection.execute('TRUNCATE cdr_temp_current_medication')
574
+ ActiveRecord::Base.connection.execute("TRUNCATE cdr_temp_patient_outcomes#{start ? '_start' : ''}")
575
+ ActiveRecord::Base.connection.execute("TRUNCATE cdr_temp_max_drug_orders#{start ? '_start' : ''}")
576
+ ActiveRecord::Base.connection.execute("TRUNCATE cdr_temp_min_auto_expire_date#{start ? '_start' : ''}")
577
+ ActiveRecord::Base.connection.execute("TRUNCATE cdr_temp_max_patient_state#{start ? '_start' : ''}")
578
+ ActiveRecord::Base.connection.execute("TRUNCATE cdr_temp_current_state#{start ? '_start' : ''}")
579
+ ActiveRecord::Base.connection.execute("TRUNCATE cdr_temp_current_medication#{start ? '_start' : ''}")
538
580
  else
539
- ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_patient_outcomes WHERE site_id = #{location}")
540
- ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_max_drug_orders WHERE site_id = #{location}")
541
- ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_min_auto_expire_date WHERE site_id = #{location}")
542
- ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_max_patient_state WHERE site_id = #{location}")
543
- ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_current_state WHERE site_id = #{location}")
544
- ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_current_medication WHERE site_id = #{location}")
581
+ ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_patient_outcomes#{start ? '_start' : ''} WHERE site_id = #{location}")
582
+ ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_max_drug_orders#{start ? '_start' : ''} WHERE site_id = #{location}")
583
+ ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_min_auto_expire_date#{start ? '_start' : ''} WHERE site_id = #{location}")
584
+ ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_max_patient_state#{start ? '_start' : ''} WHERE site_id = #{location}")
585
+ ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_current_state#{start ? '_start' : ''} WHERE site_id = #{location}")
586
+ ActiveRecord::Base.connection.execute("DELETE FROM cdr_temp_current_medication#{start ? '_start' : ''} WHERE site_id = #{location}")
545
587
  end
546
588
  end
547
589
  end
548
590
  # rubocop:enable Metrics/ClassLength
591
+ # rubocop:enable Metrics/MethodLength
549
592
  end
550
593
  end