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Oncology cancers #373

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Oncology cancers #373

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cbe75ea
feat: add breast and colorectal tables
ngarivictor Aug 20, 2023
aa72c41
fix: spelling mistake
ngarivictor Aug 21, 2023
c21a3af
feat: extraction script for breast cancer
ngarivictor Aug 27, 2023
bbb125f
fix: conflicting mappings
ngarivictor Aug 29, 2023
0c8ef08
fix: refactor concept IDs
ngarivictor Sep 12, 2023
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97 changes: 97 additions & 0 deletions omod/src/main/resources/sql/DDL.sql
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,8 @@ DROP TABLE IF EXISTS kenyaemr_etl.etl_prep_followup;
DROP TABLE IF EXISTS kenyaemr_etl.etl_progress_note;
DROP TABLE IF EXISTS kenyaemr_etl.etl_ovc_enrolment;
DROP TABLE IF EXISTS kenyaemr_etl.etl_cervical_cancer_screening;
DROP TABLE IF EXISTS kenyaemr_etl.etl_breast_cancer_screening;
DROP TABLE IF EXISTS kenyaemr_etl.etl_colorectal_cancer_screening;

DROP TABLE IF EXISTS kenyaemr_etl.etl_client_trace;
DROP TABLE IF EXISTS kenyaemr_etl.etl_contact;
Expand Down Expand Up @@ -2117,6 +2119,101 @@ CREATE TABLE kenyaemr_etl.etl_patient_program (
);
SELECT "Successfully created etl_cervical_cancer_screening table";

------------------------ creating Breast Cancer Screening Table -----------------------
CREATE TABLE kenyaemr_etl.etl_breast_cancer_screening (
uuid CHAR(38),
encounter_id INT(11) NOT NULL PRIMARY KEY,
encounter_provider INT(11),
patient_id INT(11) NOT NULL,
visit_id INT(11) DEFAULT NULL,
visit_date DATE,
location_id INT(11) DEFAULT NULL,
date_created DATETIME NOT NULL,
date_last_modified DATETIME,
visit_type VARCHAR(255) DEFAULT NULL,
screening_type VARCHAR(255) DEFAULT NULL,
post_treatment_complication_cause VARCHAR(255) DEFAULT NULL,
post_treatment_complication_other VARCHAR(255) DEFAULT NULL,
cbe_screening_method VARCHAR(255) DEFAULT NULL,
ultrasound_screening_method VARCHAR(255) DEFAULT NULL,
mammography_screening_method VARCHAR(255) DEFAULT NULL,
cbe_screening_result VARCHAR(255) DEFAULT NULL,
ultrasound_screening_result VARCHAR(255) DEFAULT NULL,
mammography_screening_result VARCHAR(255) DEFAULT NULL,
cbe_treatment_method VARCHAR(255) DEFAULT NULL,
ultrasound_treatment_method VARCHAR(255) DEFAULT NULL,
mammography_treatment_method VARCHAR(255) DEFAULT NULL,
referred_out VARCHAR(100) DEFAULT NULL,
referral_facility VARCHAR(100) DEFAULT NULL,
referral_reason VARCHAR(255) DEFAULT NULL,
followup_date DATETIME,
hiv_status VARCHAR(100) DEFAULT NULL,
smoke_cigarattes VARCHAR(255) DEFAULT NULL,
other_forms_tobacco VARCHAR(255) DEFAULT NULL,
take_alcohol VARCHAR(255) DEFAULT NULL,
previous_treatment VARCHAR(255) DEFAULT NULL,
previous_treatment_specify VARCHAR(255) DEFAULT NULL,
signs_symptoms VARCHAR(500) DEFAULT NULL,
signs_symptoms_specify VARCHAR(500) DEFAULT NULL,
family_history VARCHAR(100) DEFAULT NULL,
number_of_years_smoked VARCHAR(100) DEFAULT NULL,
number_of_cigarette_per_day VARCHAR(100) DEFAULT NULL,
clinical_notes VARCHAR(500) DEFAULT NULL,
voided INT(11),
CONSTRAINT FOREIGN KEY (patient_id) REFERENCES kenyaemr_etl.etl_patient_demographics(patient_id),
CONSTRAINT unique_uuid UNIQUE(uuid),
INDEX(visit_date),
INDEX(patient_id),
INDEX(patient_id, visit_date)
);
SELECT "Successfully created etl_breast_cancer_screening table";

------------------------ creating Colorectal Cancer Screening Table -----------------------
CREATE TABLE kenyaemr_etl.etl_colorectal_cancer_screening (
uuid CHAR(38),
encounter_id INT(11) NOT NULL PRIMARY KEY,
encounter_provider INT(11),
patient_id INT(11) NOT NULL,
visit_id INT(11) DEFAULT NULL,
visit_date DATE,
location_id INT(11) DEFAULT NULL,
date_created DATETIME NOT NULL,
date_last_modified DATETIME,
visit_type VARCHAR(255) DEFAULT NULL,
screening_type VARCHAR(255) DEFAULT NULL,
post_treatment_complication_cause VARCHAR(255) DEFAULT NULL,
post_treatment_complication_other VARCHAR(255) DEFAULT NULL,
fecal_occult_blood_test_screening_method VARCHAR(255) DEFAULT NULL,
colonoscopy_screening_method VARCHAR(255) DEFAULT NULL,
fecal_occult_blood_test_screening_result VARCHAR(255) DEFAULT NULL,
colonoscopy_screening_result VARCHAR(255) DEFAULT NULL,
fecal_occult_blood_test_treatment_method VARCHAR(255) DEFAULT NULL,
colonoscopy_treatment_method VARCHAR(255) DEFAULT NULL,
referred_out VARCHAR(100) DEFAULT NULL,
referral_facility VARCHAR(100) DEFAULT NULL,
referral_reason VARCHAR(255) DEFAULT NULL,
followup_date DATETIME,
hiv_status VARCHAR(100) DEFAULT NULL,
smoke_cigarattes VARCHAR(255) DEFAULT NULL,
other_forms_tobacco VARCHAR(255) DEFAULT NULL,
take_alcohol VARCHAR(255) DEFAULT NULL,
previous_treatment VARCHAR(255) DEFAULT NULL,
previous_treatment_specify VARCHAR(255) DEFAULT NULL,
signs_symptoms VARCHAR(500) DEFAULT NULL,
signs_symptoms_specify VARCHAR(500) DEFAULT NULL,
family_history VARCHAR(100) DEFAULT NULL,
number_of_years_smoked VARCHAR(100) DEFAULT NULL,
number_of_cigarette_per_day VARCHAR(100) DEFAULT NULL,
clinical_notes VARCHAR(500) DEFAULT NULL,
voided INT(11),
CONSTRAINT FOREIGN KEY (patient_id) REFERENCES kenyaemr_etl.etl_patient_demographics(patient_id),
CONSTRAINT unique_uuid UNIQUE(uuid),
INDEX(visit_date),
INDEX(patient_id),
INDEX(patient_id, visit_date)
);
SELECT "Successfully created etl_colorectal_cancer_screening table";

-- --------------------- creating patient contact table -------------------------------
CREATE TABLE kenyaemr_etl.etl_patient_contact (
id INT(11),
Expand Down
172 changes: 171 additions & 1 deletion omod/src/main/resources/sql/DML.sql
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4603,7 +4603,7 @@ left join (
when 145808 then 'Presumed' when 159393 then 'Presumed' when 159008 then 'Presumed'
when 5622 then 'Other' when 1115 then 'Negative' when 664 then 'Negative' else NULL end), '' )) as colposcopy_screening_result,
max(if(o1.concept_id = 165266, (case o1.value_coded when 165381 then 'Cryotherapy postponed'when 165386 then 'Cryotherapy performed'
when 162810 then 'LEEP' when 165396 then 'Cold knife cone' when 165395 then 'Thermocoagulation'
when 162810 then 'LEEP' when 165396 then 'Cold knife cone' when 165395 then 'Thermal Coagulation'
when 165385 then 'Cryotherapy performed (single Visit)' when 159837 then 'Hysterectomy' when 165391 then 'Referred for cancer treatment'
when 1107 then 'None' when 5622 then 'Other' else "" end), "" )) as colposcopy_treatment_method
from obs o
Expand Down Expand Up @@ -4637,6 +4637,176 @@ where e.voided=0
group by e.encounter_id;
SELECT "Completed processing Cervical Cancer Screening", CONCAT("Time: ", NOW());
END $$

--------------------------- process patient etl_breast_cancer_screening ---
DROP PROCEDURE IF EXISTS sp_populate_etl_breast_cancer_screening $$
CREATE PROCEDURE sp_populate_etl_breast_cancer_screening()
BEGIN
SELECT "Processing Breast Cancer screening", CONCAT("Time: ", NOW());

insert into kenyaemr_etl.etl_breast_cancer_screening(
uuid,
encounter_id,
encounter_provider,
patient_id,
visit_id,
visit_date,
location_id,
date_created,
date_last_modified,
visit_type,
screening_type,
post_treatment_complication_cause,
post_treatment_complication_other,
cbe_screening_method,
ultrasound_screening_method,
mammography_smear_screening_method,
cbe_screening_result,
ultrasound_screening_result,
mammography_screening_result,
cbe_treatment_method,
ultrasound_treatment_method,
mammogrphy_treatment_method,
referred_out,
referral_facility,
referral_reason,
followup_date,
hiv_status,
smoke_cigarattes,
other_forms_tobacco,
take_alcohol,
previous_treatment,
previous_treatment_specify,
signs_symptoms,
signs_symptoms_specify,
family_history,
number_of_years_smoked,
number_of_cigarette_per_day,
clinical_notes,
voided
)
select
e.uuid, e.encounter_id,e.creator as provider,e.patient_id, e.visit_id, e.encounter_datetime as visit_date, e.location_id,e.date_created,
if(max(o.date_created) > min(e.date_created),max(o.date_created),NULL) as date_last_modified,
max(if(o.concept_id = 160288, (case o.value_coded when 162080 then 'Initial visit'
when 161236 then 'Routine visit'
when 165381 then 'Post treatment visit'
when 1185 then 'Treatment visit'
when 165382 then 'Post treatment complication' else "" end), "" )) as visit_type,
max(if(o.concept_id = 164181, (case o.value_coded when 164180 then 'First time screening' when 160530 then 'Rescreening'
when 165389 then 'Post treatment followup' else "" end), "" )) as screening_type,
max(if(o.concept_id=163042,o.value_text,null)) as post_treatment_complication_other,
max(if(o.concept_id=5096,o.value_datetime,null)) as followup_date,
max(if(o.concept_id=1169,(case o.value_coded when 703 then "Positive" when 664 then "Negative" when 1067 then "Unknown" else "" end),null)) as hiv_status,
max(if(o.concept_id=163201,(case o.value_coded when 1065 then "Yes" when 1066 then "No" when 158939 then "Stopped" else "" end),null)) as smoke_cigarattes,
max(if(o.concept_id=163731,(case o.value_coded when 1065 then "Yes" when 1066 then "No" when 158939 then "Stopped" else "" end),null)) as other_forms_tobacco,
max(if(o.concept_id=159449,(case o.value_coded when 1065 then "Yes" when 1066 then "No" when 167155 then "Stopped" else "" end),null)) as take_alcohol,
concat_ws(',', max(if(o.concept_id = 162964 and o.value_coded = 1107, 'None', null)),
max(if(o.concept_id = 162964 and o.value_coded = 166917, 'Chemotherapy', null)),
max(if(o.concept_id = 162964 and o.value_coded = 16117, 'Radiotherapy', null)),
max(if(o.concept_id = 162964 and o.value_coded = 160345, 'Hormonal therapy', null)),
max(if(o.concept_id = 162964 and o.value_coded = 5622, 'Other', null)),
max(if(o.concept_id = 162964 and o.value_coded = 159619, 'Surgery', null))) as previous_treatment,
max(if(o.concept_id=160632,trim(o.value_text),null)) as previous_treatment_specify,
concat_ws(',', max(if(o.concept_id = 1729 and o.value_coded = 1107, 'None', null)),
max(if(o.concept_id = 1729 and o.value_coded = 111, 'Dyspepsia', null)),
max(if(o.concept_id = 1729 and o.value_coded = 117671, 'Blood in stool', null)),
max(if(o.concept_id = 1729 and o.value_coded = 5192, 'Yellow eyes', null)),
max(if(o.concept_id = 1729 and o.value_coded = 840, 'Blood in urine', null)),
max(if(o.concept_id = 1729 and o.value_coded = 132667, 'Nose Bleeding', null)),
max(if(o.concept_id = 1729 and o.value_coded = 5954, 'Difficulty in swallowing', null)),
max(if(o.concept_id = 1729 and o.value_coded = 832, 'Weight loss', null)),
max(if(o.concept_id = 1729 and o.value_coded = 140501, 'Easy fatigability', null)),
max(if(o.concept_id = 1729 and o.value_coded = 150802, 'Abnormal vaginal bleeding', null)),
max(if(o.concept_id = 1729 and o.value_coded = 115844, 'Changing/enlarging skin moles', null)),
max(if(o.concept_id = 1729 and o.value_coded = 120551, 'Chronic skin ulcers', null)),
max(if(o.concept_id = 1729 and o.value_coded = 115919, 'Lumps/swellings', null)),
max(if(o.concept_id = 1729 and o.value_coded = 145455, 'Chronic cough', null)),
max(if(o.concept_id = 1729 and o.value_coded = 115779, 'Persistent headaches', null)),
max(if(o.concept_id = 1729 and o.value_coded = 129452, 'Post-coital bleeding', null)),
max(if(o.concept_id = 1729 and o.value_coded = 151903, 'Changing bowel habits', null)),
max(if(o.concept_id = 1729 and o.value_coded = 5622, 'Other', null))) as signs_symptoms,
max(if(o.concept_id=161011,trim(o.value_text),null)) as signs_symptoms_specify,
max(if(o.concept_id=160592,(case o.value_coded when 1065 then "Yes" when 1066 then "No" else "" end),null)) as family_history,
max(if(o.concept_id=159931,o.value_numeric,null)) as number_of_years_smoked,
max(if(o.concept_id=1546,o.value_numeric,null)) as number_of_cigarette_per_day,
max(if(o.concept_id=164879,trim(o.value_text),null)) as clinical_notes,

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 (165383,1788,163042,165267,163589,163731,159449,163201,1169,5096,1887,165268,1169,164181,160288,161011,1729,160632,162964,160592,159931,1546,164879)
inner join (
select o.person_id,
o.encounter_id,
o.obs_group_id,
max(if(o.concept_id = 159780, (case o.value_coded when 1000090 then "CBE" else "" end),
null)) as cbe_screening_method,
max(if(o.concept_id = 160606,
(case o.value_coded when 1115 then "Normal" when 1116 then "Abnormal" else "" end),
null)) as cbe_screening_result,
max(if(o.concept_id = 165070, (case o.value_coded
when 1115 then "Counseled on negative results"
when 1116 then "Refer for Tripple Assesment"
else "" end), null)) as cbe_treatment_method,
max(if(o.concept_id = 159780, (case o.value_coded when 1000092 then "Breast Ultrasound" else "" end),
null)) as ultrasound_screening_method,
max(if(o.concept_id = 160606, (case o.value_coded
when 1000094 then "Birads 0"
when 1000093 then "Birads 1"
when 1000095 then "Birads 2"
when 1000096 then "Birads 3"
when 1000097 then "Birads 4"
when 1000098 then "Birads 5"
when 1000099 then "Birads 6"
else "" end), null)) as ultrasound_screening_result,
max(if(o.concept_id in (165070, 166665, 1000145), (case o.value_coded
when 1609 then "Recall for additional imaging"
when 432 then "Routine ultrasound screening"
when 164080 then "Short-interval(6 months) follow-up"
when 136785 then "Tissue Diagnosis(U/S guided biopsy)"
when 1000103 then "Refer for further management"
when 1267 then "Done"
when 1118 then "Not done"
when 1000078
then "Negative-Counsel on negative results and review (provide review date)"
when 1000088 then "Date screening done"
when 160632 then "Reason not done"
else "" end), null)) as ultrasound_treatment_method,
max(if(o.concept_id = 159780, (case o.value_coded when 163591 then "Mammography" else "" end),
null)) as mammography_screening_method,
max(if(o.concept_id = 160606, (case o.value_coded
when 1000094 then "Birads 0"
when 1000093 then "Birads 1"
when 1000095 then "Birads 2"
when 1000096 then "Birads 3"
when 1000097 then "Birads 4"
when 1000098 then "Birads 5"
when 1000099 then "Birads 6"
else "" end), null)) as mammography_screening_result,
max(if(o.concept_id in (165070, 166665, 1000145), (case o.value_coded
when 1609 then "Recall for additional imaging"
when 432 then "Routine mammography screening"
when 164080 then "Short-interval(6 months) follow-up"
when 136785 then "Tissue Diagnosis(U/S guided biopsy)"
when 1000103 then "Refer for further management"
when 159619
then "Surgical excision when clinically appropriate)"
else "" end), null)) as mammography_treatment_method
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 (159780, 160606, 165070, 1272, 166665, 1000145)
and o.voided = 0
group by e.encounter_id, o.obs_group_id
)
where e.voided=0
group by e.encounter_id;
SELECT "Completed processing Breast Cancer Screening", CONCAT("Time: ", NOW());
END $$

--------------------------- process patient contact ------------------------

DROP PROCEDURE IF EXISTS sp_populate_etl_patient_contact $$
Expand Down