Merge pull request #17 from PIH/UHM-6397-rename-columns-to-zlemrid-on…

…-all-haiti-warehouse Uhm 6397 rename columns to zlemrid on all haiti warehouse
PIH · Apr 15, 2022 · 9daad22 · 9daad22
2 parents 2b4c91d + edecdd9
commit 9daad22
Show file tree

Hide file tree

Showing 63 changed files with 149 additions and 113 deletions.
diff --git a/jobs/sql/extractions/covid_admission.sql b/jobs/sql/extractions/covid_admission.sql
@@ -172,7 +172,7 @@ UPDATE temp_covid_admission_encounter SET contact_case_14d = OBS_VALUE_CODED_LIS
 ## EXECUTE FINAL SELECTION
 SELECT
 	encounter_id,
-	patient_id,
+	zlemr(patient_id),
 	encounter_datetime,
     date_entered,
     user_entered,

diff --git a/jobs/sql/extractions/covid_diagnoses.sql b/jobs/sql/extractions/covid_diagnoses.sql
@@ -211,7 +211,7 @@ ORDER BY person_id;
 
 ##### FINAL QUERY EXECUTION
 SELECT
-  ce.patient_id,
+  zlemr(ce.patient_id),
   ce.encounter_id,
   ce.encounter_type,
   ce.location,
@@ -230,4 +230,4 @@ LEFT JOIN
 temp_covid_diagnosis_confirmation dc ON d.obs_group_id = dc.obs_group_id AND d.encounter_id = dc.encounter_id
 LEFT JOIN
 temp_covid_diagnosis_order dor ON d.obs_group_id = dor.obs_group_id AND d.encounter_id = dor.encounter_id
-ORDER BY ce.patient_id;
+ORDER BY ce.patient_id;
diff --git a/jobs/sql/extractions/covid_discharge.sql b/jobs/sql/extractions/covid_discharge.sql
@@ -122,7 +122,7 @@ UPDATE temp_covid_discharge SET other_medications = OBS_VALUE_TEXT(encounter_id,
 ### Final query
 SELECT
       encounter_id,
-      patient_id,
+      zlemr(patient_id),
       encounter_date,
       encounter_type,
       date_entered,

diff --git a/jobs/sql/extractions/covid_disposition.sql b/jobs/sql/extractions/covid_disposition.sql
@@ -106,7 +106,7 @@ FROM (SELECT
         ) index_descending );
 
 SELECT
-	tcd.patient_id patient_id,
+	zlemr(tcd.patient_id) emr_id,
 	tcd.encounter_id encounter_id,
 	encounter_type,
 	location,

diff --git a/jobs/sql/extractions/covid_lab_test.sql b/jobs/sql/extractions/covid_lab_test.sql
@@ -330,7 +330,7 @@ UPDATE temp_covid_lab_app_result tcl INNER JOIN temp_final_covid_lab_encounters
 DROP TEMPORARY TABLE IF EXISTS temp_final_query;
 CREATE TEMPORARY TABLE temp_final_query AS
 SELECT
-    ls.person_id patient_id,
+    zlemr(ls.person_id) emr_id,
     ls.encounter_id encounter_id,
     ls.obs_id,
     e.encounter_date,
@@ -362,4 +362,4 @@ FROM
 ORDER BY ls.person_id, ls.encounter_id, lspd.value_datetime;
 
 SELECT * FROM
-    (SELECT * FROM temp_final_query q UNION ALL SELECT * FROM temp_covid_lab_app_result r) a;
+    (SELECT * FROM temp_final_query q UNION ALL SELECT * FROM temp_covid_lab_app_result r) a;
diff --git a/jobs/sql/extractions/covid_visit.sql b/jobs/sql/extractions/covid_visit.sql
@@ -1066,7 +1066,7 @@ create index temp_index_desc_ei on temp_index_desc(encounter_id);
 
 #### Final query
 SELECT
-        tcv.patient_id patient_id,
+        zlemr(tcv.patient_id) emr_id,
         tcv.encounter_id encounter_id,
         encounter_date,
         location,

diff --git a/jobs/sql/extractions/hiv_dispensing.sql b/jobs/sql/extractions/hiv_dispensing.sql
@@ -313,7 +313,7 @@ where t.dispense_date_descending = 1;
 
 # final query
 Select
-t.patient_id,
+zlemr(t.patient_id),
 t.encounter_id,
 t.dispense_date,
 t.dispense_site,
@@ -355,4 +355,4 @@ t.regimen_match,
 dispense_date_ascending,
 dispense_date_descending
 from temp_HIV_dispensing t
-order by patient_id, dispense_date asc, encounter_id asc;
+order by patient_id, dispense_date asc, encounter_id asc;
diff --git a/jobs/sql/extractions/hiv_monthly_reporting.sql b/jobs/sql/extractions/hiv_monthly_reporting.sql
@@ -153,7 +153,6 @@ update temp_eom_appts t
 set latest_arv_dispensed_line = obs_value_coded_list(t.latest_arv_dispensed_id, 'PIH','13115',@locale );
 
 SELECT
-	patient_id,
 	zlemr(patient_id),
 	date_enrolled ,
 	date_completed ,

diff --git a/jobs/sql/extractions/hiv_patient.sql b/jobs/sql/extractions/hiv_patient.sql
@@ -626,7 +626,6 @@ UPDATE temp_hiv_art t set art_regimen = ActiveDrugConceptNameList(t.patient_id,
 
 ### Final Query
 SELECT 
-t.patient_id,
 t.zl_emr_id,
 t.hivemr_v1_id,
 t.hiv_dossier_id,

diff --git a/jobs/sql/extractions/hiv_patient_program.sql b/jobs/sql/extractions/hiv_patient_program.sql
@@ -34,7 +34,7 @@ set location = location_name(location_id),
 
 select
        patient_program_id,
-       patient_id,
+       zlemr(patient_id),
        date_enrolled,
        date_completed,
        location,

diff --git a/jobs/sql/extractions/hiv_regimens.sql b/jobs/sql/extractions/hiv_regimens.sql
@@ -293,7 +293,7 @@ where t.index_descending_category = 1 and t.drug_category = 'ART';
 select
 order_id,    
 previous_order_id,
-patient_id,
+zlemr(patient_id),
 order_action,
 encounter_id,
 encounter_datetime,

diff --git a/jobs/sql/extractions/hiv_status.sql b/jobs/sql/extractions/hiv_status.sql
@@ -245,7 +245,7 @@ SET transfer_internal_sitename = LOCATION_NAME(th.location_id);
 ### Final query
 SELECT 
     status_id,
-    patient_id,
+    zlemr(patient_id),
     ZLEMR(patient_id) "zl_emr_id",
     LOCATION_NAME(location_id) "patient_location",
     transfer_internal_sitename,

diff --git a/jobs/sql/extractions/hiv_tests.sql b/jobs/sql/extractions/hiv_tests.sql
@@ -166,14 +166,18 @@ create index temp_hiv_lab_index_asc_test_type on temp_hiv_lab_index_asc(test_typ
 create index temp_hiv_lab_index_desc_encounter_id on temp_hiv_lab_index_desc(encounter_id);
 create index temp_hiv_lab_index_desc_test_type on temp_hiv_lab_index_desc(test_type);	
 
+create index temp_hiv_lab_index_asc_encounter_id on temp_hiv_lab_index_asc(encounter_id);
+create index temp_hiv_lab_index_asc_test_type on temp_hiv_lab_index_asc(test_type);
+create index temp_hiv_lab_index_desc_encounter_id on temp_hiv_lab_index_desc(encounter_id);
+create index temp_hiv_lab_index_desc_test_type on temp_hiv_lab_index_desc(test_type);
+
 UPDATE temp_lab_tests_final tbf JOIN temp_hiv_lab_index_asc tbia ON tbf.encounter_id = tbia.encounter_id AND tbf.test_type = tbia.test_type
 SET tbf.index_asc = tbia.index_asc;
 
 UPDATE temp_lab_tests_final tbf JOIN temp_hiv_lab_index_desc tbia ON tbf.encounter_id = tbia.encounter_id AND tbf.test_type = tbia.test_type
 SET tbf.index_desc = tbia.index_desc;
 
 SELECT
-	person_id,
     emr_id,
     patient_identifier(person_id, '139766e8-15f5-102d-96e4-000c29c2a5d7') hivemr_v1_id,
     encounter_id,

diff --git a/jobs/sql/extractions/hiv_viral_load.sql b/jobs/sql/extractions/hiv_viral_load.sql
@@ -130,7 +130,7 @@ FROM (SELECT
 
 ### Final query
 SELECT
-        tvl.patient_id,
+        zlemr(tvl.patient_id),
         tvl.encounter_id,
         tvl.visit_location,
         tvl.date_entered,

diff --git a/jobs/sql/extractions/hiv_visit.sql b/jobs/sql/extractions/hiv_visit.sql
@@ -101,4 +101,17 @@ update temp_hiv_visit t
 inner join temp_visit_index_desc tvid on tvid.encounter_id = t.encounter_id
 set t.index_desc = tvid.index_desc;
 
-SELECT * FROM temp_hiv_visit;
+SELECT 
+encounter_id,
+emr_id,
+hivemr_v1,	
+encounter_type,
+date_entered,
+user_entered,
+pregnant,
+visit_date,
+next_visit_date,
+visit_location,
+index_asc,
+index_desc
+FROM temp_hiv_visit;
diff --git a/jobs/sql/extractions/mch_birth.sql b/jobs/sql/extractions/mch_birth.sql
@@ -136,7 +136,7 @@ UPDATE temp_mch_birth_final SET mother_emr_id = ZLEMR(patient_id);
 UPDATE temp_mch_birth_final tf SET multiples = (SELECT COUNT(patient_id) FROM temp_mch_birth_stage ts WHERE tf.encounter_id = ts.encounter_id GROUP BY ts.encounter_id);
 
 SELECT
-patient_id,
+zlemr(patient_id),
 mother_emr_id,
 encounter_date,
 date_entered,
@@ -148,4 +148,4 @@ birth_outcome,
 birth_weight,
 birth_neonatal_resuscitation,
 birth_macerated_fetus
-FROM temp_mch_birth_final ORDER BY patient_id, encounter_id, birth_number;
+FROM temp_mch_birth_final ORDER BY patient_id, encounter_id, birth_number;
diff --git a/jobs/sql/extractions/mch_j9_data.sql b/jobs/sql/extractions/mch_j9_data.sql
@@ -269,7 +269,7 @@ set prenatal_teas = value_coded_name(latest_obs(t.patient_id, 'PIH','13737'),@lo
 
 -- final output
 Select
-patient_id,
+zlemr(patient_id),
 patient_age,
 education_level,
 able_read_write,

diff --git a/jobs/sql/extractions/mch_patient.sql b/jobs/sql/extractions/mch_patient.sql
@@ -178,8 +178,7 @@ UPDATE temp_mch_patient tm SET tm.dossier_id = dosId(tm.patient_id);
 
 ### Final query
 SELECT
-    patient_id,
-    mch_emr_id                      pih_emr_id,
+    mch_emr_id                      emr_id,
     dossier_id                      dossier_id,
     initial_encounter_type_name     first_encounter_type,
     encounter_type_name             last_encounter_type,
@@ -200,4 +199,4 @@ SELECT
     antenatal_visit,
     estimated_delivery_date,
     pregnant
-FROM temp_mch_patient;
+FROM temp_mch_patient;
diff --git a/jobs/sql/extractions/mch_pregnancy.sql b/jobs/sql/extractions/mch_pregnancy.sql
@@ -114,4 +114,50 @@ UPDATE temp_mch_pregnancy t SET pregnancy_10_outcome = OBS_FROM_GROUP_ID_VALUE_C
 UPDATE temp_mch_pregnancy t SET pmtct_club = OBS_VALUE_CODED_LIST(t.encounter_id, 'PIH', '13262', 'en');
 UPDATE temp_mch_pregnancy t SET  delivery_location_plan = OBS_VALUE_CODED_LIST(t.encounter_id, 'CIEL', '159758', 'en');
 
-SELECT * FROM temp_mch_pregnancy;
+SELECT
+pregnancy_id,
+encounter_id,
+emr_id,
+encounter_date,
+date_entered,
+user_entered,
+gravidity,
+parity,
+num_abortions,
+num_living_children,
+last_period_date,
+expected_delivery_date,
+calculated_gestational_age,
+pregnancy_1_birth_order,
+pregnancy_1_delivery_type,
+pregnancy_1_outcome,
+pregnancy_2_birth_order,
+pregnancy_2_delivery_type,
+pregnancy_2_outcome,
+pregnancy_3_birth_order,
+pregnancy_3_delivery_type,
+pregnancy_3_outcome,
+pregnancy_4_birth_order,
+pregnancy_4_delivery_type,
+pregnancy_4_outcome,
+pregnancy_5_birth_order,
+pregnancy_5_delivery_type,
+pregnancy_5_outcome,
+pregnancy_6_birth_order,
+pregnancy_6_delivery_type,
+pregnancy_6_outcome,
+pregnancy_7_birth_order,
+pregnancy_7_delivery_type,
+pregnancy_7_outcome,
+pregnancy_8_birth_order,
+pregnancy_8_delivery_type,
+pregnancy_8_outcome,
+pregnancy_9_birth_order,
+pregnancy_9_delivery_type,
+pregnancy_9_outcome,
+pregnancy_10_birth_order,
+pregnancy_10_delivery_type,
+pregnancy_10_outcome,
+pmtct_club,
+delivery_location_plan
+FROM temp_mch_pregnancy;
diff --git a/jobs/sql/extractions/mch_status.sql b/jobs/sql/extractions/mch_status.sql
@@ -47,14 +47,7 @@ patient_id IN (
 
 -- ZL EMR ID
 UPDATE temp_mch_status t
-INNER JOIN
-   (SELECT patient_id, GROUP_CONCAT(identifier) 'ids'
-    FROM patient_identifier pid
-    WHERE pid.voided = 0
-    AND pid.identifier_type = @mch_emr_id
-    GROUP BY patient_id
-   ) ids ON ids.patient_id = t.patient_id
-SET t.mch_emr_id = ids.ids;
+SET t.mch_emr_id = zlemr(t.patient_id);
 
 ######### index count
 ########## indexes
@@ -228,7 +221,6 @@ SET tmp.encounter_location_name	= tme.encounter_location_name,
 
 ### Final Query
 SELECT
-    patient_id,
     mch_emr_id,
     enrollment_location,
     encounter_location_name,

diff --git a/jobs/sql/extractions/mch_visit.sql b/jobs/sql/extractions/mch_visit.sql
@@ -791,7 +791,6 @@ SET
     fp_counseling_received = OBS_VALUE_CODED_LIST(te.encounter_id, 'CIEL', '165309', 'en');
 
 SELECT 
-    patient_id,
     ZLEMR(patient_id),
     encounter_id,
     visit_date,
@@ -858,4 +857,4 @@ SELECT
     index_desc
 FROM
     temp_obgyn_visit
-ORDER BY patient_id , index_asc;
+ORDER BY patient_id , index_asc;
diff --git a/jobs/sql/extractions/ovc_program_encounters.sql b/jobs/sql/extractions/ovc_program_encounters.sql
@@ -525,7 +525,6 @@ select * from temp_program_no_statuses_encounters;
 
 ###### Final query #######
 SELECT
-    person_id,
 	ZLEMR(person_id),
 	patient_program_id,
 	LOCATION_NAME(location_id),
@@ -549,4 +548,4 @@ SELECT
 	index_desc_program_status,
 	index_asc_enrollment,
 	index_desc_enrollment
- FROM temp_ovc_program_status_encounters ORDER BY person_id, patient_program_id, state, encounter_date;
+ FROM temp_ovc_program_status_encounters ORDER BY person_id, patient_program_id, state, encounter_date;
diff --git a/jobs/sql/extractions/pmtct_contacts.sql b/jobs/sql/extractions/pmtct_contacts.sql
@@ -81,7 +81,6 @@ update temp_contacts t inner join obs o on t.concept_obs_group_id = o.obs_id
 set t.date_entered = o.date_created, t.user_entered = username(o.creator);
 
 select 
-patient_id,
 zlemrid,
 age,
 hiv_enrollment_date,

diff --git a/jobs/sql/extractions/pmtct_infant_delivery.sql b/jobs/sql/extractions/pmtct_infant_delivery.sql
@@ -124,7 +124,6 @@ set health_facility = (select location_name(value_text) from obs where voided =
 update temp_eid t set t.breastfeeding_status = value_coded_name(latest_obs(t.patient_id, 'CIEL', '1151'), 'en');
 
 select  
-patient_id,
 zlemr(patient_id),
 infant_age_in_months,
 age_cat_infant,

diff --git a/jobs/sql/extractions/pmtct_labs.sql b/jobs/sql/extractions/pmtct_labs.sql
@@ -96,7 +96,6 @@ order by patient_id asc, test_date desc, obs_id desc;
 
 -- final output
 select 
-patient_id,
 zlemr(patient_id),
 test_date,
 test_result_date,

diff --git a/jobs/sql/extractions/pmtct_pregnancy.sql b/jobs/sql/extractions/pmtct_pregnancy.sql
@@ -211,7 +211,6 @@ UPDATE temp_pmtct_pregnancy t SET index_desc = (SELECT index_desc FROM temp_pmtc
 
 ## final query
 SELECT 
-	patient_id,
     zlemr,
     start_date,
     pmtct_enrollment_date,
@@ -228,4 +227,4 @@ SELECT
     hiv_known_before_current_pregnancy,
     index_asc,
     index_desc
-FROM temp_pmtct_pregnancy;
+FROM temp_pmtct_pregnancy;
diff --git a/jobs/sql/extractions/pmtct_visits.sql b/jobs/sql/extractions/pmtct_visits.sql
@@ -183,4 +183,17 @@ CREATE TEMPORARY TABLE temp_pmtct_visit_index_desc
 UPDATE temp_pmtct_visit t SET t.index_asc = (SELECT index_asc FROM temp_pmtct_visit_index_asc a WHERE t.visit_id = a.visit_id);
 UPDATE temp_pmtct_visit t SET t.index_desc = (SELECT index_desc FROM temp_pmtct_visit_index_desc b WHERE t.visit_id = b.visit_id);
 
-SELECT * FROM temp_pmtct_visit ORDER BY patient_id, visit_date, visit_id;
+SELECT 
+visit_id,
+encounter_id,
+emr_id,
+visit_date,
+health_facility,
+date_entered,
+user_entered,
+hiv_test_date,
+tb_screening_date,
+has_provided_contact,
+index_asc,
+index_desc
+FROM temp_pmtct_visit ORDER BY patient_id, visit_date, visit_id;
diff --git a/jobs/sql/extractions/tb_lab_results.sql b/jobs/sql/extractions/tb_lab_results.sql
@@ -378,7 +378,6 @@ UPDATE temp_tb_final_query tbf
 
 ## Final query
 SELECT
-    patient_id,
     zlemr(patient_id),
     dosId(patient_id),
     encounter_id,

diff --git a/jobs/sql/extractions/tb_screening.sql b/jobs/sql/extractions/tb_screening.sql
@@ -150,7 +150,6 @@ SET t.index_descending = tsid.index_desc;
 
 
 SELECT
-patient_id,
 ZLEMR(patient_id) emr_id,
 DOSID(patient_id) dossier_id,
 encounter_id,