Merge pull request #387 from makombe/retinoblastoma

Add retinoblastoma cancer type
palladiumkenya · Oct 11, 2023 · 0e451ae · 0e451ae
2 parents 642c1e0 + 8efddf7
commit 0e451ae
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Showing 4 changed files with 67 additions and 5 deletions.
diff --git a/omod/src/main/resources/sql/DDL.sql b/omod/src/main/resources/sql/DDL.sql
@@ -2106,6 +2106,15 @@ CREATE TABLE kenyaemr_etl.etl_patient_program (
     colonoscopy_method_results VARCHAR(255) DEFAULT NULL,
     fecal_occult_screening_treatment VARCHAR(255) DEFAULT NULL,
     colonoscopy_method_treatment VARCHAR(255) DEFAULT NULL,
+
+    retinoblastoma_cancer VARCHAR(255) DEFAULT NULL,
+    retinoblastoma_eua_screening_method VARCHAR(255) DEFAULT NULL,
+    retinoblastoma_gene_method VARCHAR(255) DEFAULT NULL,
+    retinoblastoma_eua_screening_results VARCHAR(255) DEFAULT NULL,
+    retinoblastoma_gene_method_results VARCHAR(255) DEFAULT NULL,
+    retinoblastoma_eua_treatment VARCHAR(255) DEFAULT NULL,
+    retinoblastoma_gene_treatment VARCHAR(255) DEFAULT NULL,
+
     referred_out VARCHAR(100) DEFAULT NULL,
     referral_facility VARCHAR(100) DEFAULT NULL,
     referral_reason VARCHAR(255) DEFAULT NULL,

diff --git a/omod/src/main/resources/sql/DML.sql b/omod/src/main/resources/sql/DML.sql
@@ -4422,6 +4422,13 @@ insert into kenyaemr_etl.etl_cervical_cancer_screening(
     colonoscopy_method_results,
     fecal_occult_screening_treatment,
     colonoscopy_method_treatment,
+    retinoblastoma_cancer,
+    retinoblastoma_eua_screening_method,
+    retinoblastoma_gene_method,
+    retinoblastoma_eua_screening_results,
+    retinoblastoma_gene_method_results,
+    retinoblastoma_eua_treatment,
+    retinoblastoma_gene_treatment,
     referred_out,
     referral_facility,
     referral_reason,
@@ -4495,6 +4502,18 @@ select
                                   when 1000143 then "Refer for biopsy"
                                   when 1000103 then "Referred for further management"
                                   when 162907 then "Refer to surgical resection" else "" end),null)) as colonoscopy_method_treatment,
+
+      max(if(o.concept_id = 116030 and o.value_coded = 127527, 'Yes', null))as retinoblastoma_cancer,
+      max(if(o.concept_id = 163589 and o.value_coded = 1000149, 'EUA(Examination Under Anesthesia)', null))as retinoblastoma_eua_screening_method,
+      max(if(o.concept_id = 163589 and o.value_coded = 1000105, 'Retinoblastoma gene (RB1 gene)', null))as retinoblastoma_gene_method,
+      max(if(o.concept_id=1000149, (case o.value_coded when 1115 then "Normal" when 1116 then "Abnormal" else "" end),null)) as retinoblastoma_eua_screening_results ,
+      max(if(o.concept_id=1000105, (case o.value_coded when 703 then "Negative"
+                                   when 664 then "Positive" else "" end),null)) as retinoblastoma_gene_method_results,
+     max(if(o.concept_id = 1000149, (case o.value_coded when 1000078 then "Counsel on negative findings"
+                                    when 1000121 then "Referred for further evaluation" else "" end),null)) as retinoblastoma_eua_treatment,
+     max(if(o.concept_id = 1000150, (case o.value_coded when 1000078 then "Counsel on negative findings"
+                                  when 1000121 then "Referred for further evaluation" else "" end),null)) as retinoblastoma_gene_treatment,
+
      max(if(o.concept_id in (1788,165267),(case o.value_coded when 1065 then "Yes" when 1066 then "No" else "" end),null)) as referred_out,
      max(if(o.concept_id=165268,o.value_text,null)) as referral_facility,
      max(if(o.concept_id = 1887, (case o.value_coded when 165388 then 'Site does not have cryotherapy machine'
@@ -4543,7 +4562,8 @@ e.voided
 from encounter e
 	inner join person p on p.person_id=e.patient_id and p.voided=0
 	inner join form f on f.form_id=e.form_id and f.uuid in ("be5c5602-0a1d-11eb-9e20-37d2e56925ee","0c93b93c-bfef-4d2a-9fbe-16b59ee366e7")
-inner join obs o on o.encounter_id = e.encounter_id and o.concept_id in (165383,1788,163042,116030,164959,166664,1000147,1000148,165267,163589,163731,159449,163201,1169,5096,1887,165268,1169,164181,160288,161011,1729,160632,162964,160592,159931,1546,164879)
+inner join obs o on o.encounter_id = e.encounter_id and o.concept_id in (165383,1788,163042,116030,164959,166664,1000147,1000148,165267,163589,163731,159449,163201,1169,5096,1887,165268,1169,164181,
+160288,161011,1729,160632,162964,160592,159931,1546,164879,163589,1000149, 1000105,1000150)
 inner join (
              select
                o.person_id,
@@ -4586,7 +4606,7 @@ inner join (
              from obs o
              inner join encounter e on e.encounter_id = o.encounter_id
              inner join form f on f.form_id=e.form_id and f.uuid in ("be5c5602-0a1d-11eb-9e20-37d2e56925ee","0c93b93c-bfef-4d2a-9fbe-16b59ee366e7")
-             where o.concept_id in (163589, 164934, 116030, 165070,160705,165266,166937,1272,166665,159362,1000148,163591) and o.voided=0
+             where o.concept_id in (163589, 164934, 116030, 165070,160705,165266,166937,1272,166665,159362,1000148,163591,1000149,1000105) and o.voided=0
              group by e.encounter_id, o.obs_group_id
            ) t on e.encounter_id = t.encounter_id
 left join (

diff --git a/omod/src/main/resources/sql/DataTools.sql b/omod/src/main/resources/sql/DataTools.sql
@@ -1900,6 +1900,13 @@ create table kenyaemr_datatools.cervical_cancer_screening as
     hpv_treatment_method,
     pap_smear_treatment_method,
     via_vili_treatment_method,
+    retinoblastoma_cancer,
+    retinoblastoma_eua_screening_method,
+    retinoblastoma_gene_method,
+    retinoblastoma_eua_screening_results,
+    retinoblastoma_gene_method_results,
+    retinoblastoma_eua_treatment,
+    retinoblastoma_gene_treatment,
     referred_out,
     referral_facility,
     referral_reason,

diff --git a/omod/src/main/resources/sql/Scheduled_Updates.sql b/omod/src/main/resources/sql/Scheduled_Updates.sql
@@ -4547,6 +4547,13 @@ CREATE PROCEDURE sp_update_etl_cervical_cancer_screening(IN last_update_time DAT
     hpv_treatment_method,
     pap_smear_treatment_method,
     via_vili_treatment_method,
+    retinoblastoma_cancer,
+    retinoblastoma_eua_screening_method,
+    retinoblastoma_gene_method,
+    retinoblastoma_eua_screening_results,
+    retinoblastoma_gene_method_results,
+    retinoblastoma_eua_treatment,
+    retinoblastoma_gene_treatment,
     referred_out,
     referral_facility,
     referral_reason,
@@ -4604,6 +4611,17 @@ select
 	    if(t.pap_smear_treatment_method is not null and f.uuid="be5c5602-0a1d-11eb-9e20-37d2e56925ee", t.pap_smear_treatment_method, null))) as pap_smear_treatment_method,
      max(if(t1.via_vili_treatment_method is not null and f.uuid = "0c93b93c-bfef-4d2a-9fbe-16b59ee366e7", t1.via_vili_treatment_method,
 	    if(t.via_vili_treatment_method is not null and f.uuid="be5c5602-0a1d-11eb-9e20-37d2e56925ee", t.via_vili_treatment_method, null))) as via_vili_treatment_method,
+     max(if(o.concept_id = 116030 and o.value_coded = 127527, 'Yes', null))as retinoblastoma_cancer,
+      max(if(o.concept_id = 163589 and o.value_coded = 1000149, 'EUA(Examination Under Anesthesia)', null))as retinoblastoma_eua_screening_method,
+      max(if(o.concept_id = 163589 and o.value_coded = 1000105, 'Retinoblastoma gene (RB1 gene)', null))as retinoblastoma_gene_method,
+      max(if(o.concept_id=1000149, (case o.value_coded when 1115 then "Normal" when 1116 then "Abnormal" else "" end),null)) as retinoblastoma_eua_screening_results ,
+      max(if(o.concept_id=1000105, (case o.value_coded when 703 then "Negative"
+                                   when 664 then "Positive" else "" end),null)) as retinoblastoma_gene_method_results,
+     max(if(o.concept_id = 1000149, (case o.value_coded when 1000078 then "Counsel on negative findings"
+                                    when 1000121 then "Referred for further evaluation" else "" end),null)) as retinoblastoma_eua_treatment,
+     max(if(o.concept_id = 1000150, (case o.value_coded when 1000078 then "Counsel on negative findings"
+                                  when 1000121 then "Referred for further evaluation" else "" end),null)) as retinoblastoma_gene_treatment,
+
 
      max(if(o.concept_id in (1788,165267),(case o.value_coded when 1065 then "Yes" when 1066 then "No" else "" end),null)) as referred_out,
      max(if(o.concept_id=165268,o.value_text,null)) as referral_facility,
@@ -4653,7 +4671,7 @@ e.voided
 from encounter e
 	inner join person p on p.person_id=e.patient_id and p.voided=0
 	inner join form f on f.form_id=e.form_id and f.uuid in ("be5c5602-0a1d-11eb-9e20-37d2e56925ee","0c93b93c-bfef-4d2a-9fbe-16b59ee366e7")
-inner join obs o on o.encounter_id = e.encounter_id and o.concept_id in (165383,1788,165267,163589,163042,116030,163731,159449,163201,1169,5096,1887,165268,1169,164181,160288,161011,1729,160632,162964,160592,159931,1546,164879)
+inner join obs o on o.encounter_id = e.encounter_id and o.concept_id in (165383,1788,165267,163589,163042,116030,163731,159449,163201,1169,5096,1887,165268,1169,164181,160288,161011,1729,160632,162964,160592,159931,1546,164879,163589,1000149, 1000105,1000150)
 inner join (
              select
                o.person_id,
@@ -4696,7 +4714,7 @@ inner join (
              from obs o
              inner join encounter e on e.encounter_id = o.encounter_id
              inner join form f on f.form_id=e.form_id and f.uuid in ("be5c5602-0a1d-11eb-9e20-37d2e56925ee","0c93b93c-bfef-4d2a-9fbe-16b59ee366e7")
-             where o.concept_id in (163589, 164934, 165070,160705,165266,166937,1272,166665) and o.voided=0
+             where o.concept_id in (163589, 164934, 165070,160705,165266,166937,1272,166665, 1000149,1000105) and o.voided=0
              group by e.encounter_id, o.obs_group_id
            ) t on e.encounter_id = t.encounter_id
 left join (
@@ -4792,7 +4810,15 @@ colposcopy_screening_result=VALUES(colposcopy_screening_result),hpv_screening_re
 pap_smear_screening_result=VALUES(pap_smear_screening_result),via_vili_screening_result=VALUES(via_vili_screening_result),
 colposcopy_treatment_method=VALUES(colposcopy_treatment_method),hpv_treatment_method=VALUES(hpv_treatment_method),
 pap_smear_treatment_method=VALUES(pap_smear_treatment_method),via_vili_treatment_method=VALUES(via_vili_treatment_method),
-referred_out=VALUES(referred_out),referral_facility=VALUES(referral_facility),
+referred_out=VALUES(referred_out),
+retinoblastoma_cancer=VALUES(retinoblastoma_cancer),
+retinoblastoma_eua_screening_method=VALUES(retinoblastoma_eua_screening_method),
+retinoblastoma_gene_method=VALUES(retinoblastoma_gene_method),
+retinoblastoma_eua_screening_results=VALUES(retinoblastoma_eua_screening_results),
+retinoblastoma_gene_method_results=VALUES(retinoblastoma_gene_method_results),
+retinoblastoma_eua_treatment=VALUES(retinoblastoma_eua_treatment),
+retinoblastoma_gene_treatment=VALUES(retinoblastoma_gene_treatment),
+referral_facility=VALUES(referral_facility),
 referral_reason=VALUES(referral_reason),followup_date=VALUES(followup_date),hiv_status=VALUES(hiv_status),
 smoke_cigarattes=VALUES(smoke_cigarattes),other_forms_tobacco=VALUES(other_forms_tobacco),
 take_alcohol=VALUES(take_alcohol),previous_treatment=VALUES(previous_treatment),