esaude/emr-to-mozart-etl

Name: emr-to-mozart-etl

Owner: eSaude

Description: Tool for data conversion from OpenMRS EMR to MozART

Created: 2017-10-02 15:27:34.0

Updated: 2017-10-02 15:27:34.0

Pushed: 2017-12-19 11:44:16.0

Homepage: null

Size: 358

Language: null

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README

emr-to-mozart-etl

Executar o job via linha de comando

./kitchen.sh -file /home/edrisse/emr-to-mozart-etl/migrate-data.kjb

TODO

Conversar com Valério sobre introduzir limpeza de dados automatizada;

Colocar a migração como container do Docker;

Criar esquema export_db como um passo do Job do PDI;

Adicionar verificações de dados como Job do PDI;

Quando dá erro ao importar bases grandes no MySQL

set global max_allowed_packet=51210241024;

mysqldump -u root -p –no-data –skip-comments openmrs > /home/openmrs-structure.sql

insert into global_property (property, property_value, uuid) values ('esaudemetadata.hfc', '92001', '52128fe7-0aaa-4452-9c01-124bd5cd6517'); insert into global_property (property, property_value, uuid) values ('esaudemetadata.dateToImportTo', '2017-02-10', '66536be7-3c3b-407d-97cd-d39d5253ff87');

update person set person.voided = true where person.birthdate is null; update patient_program set voided = true where patient_program.patient_program_id = 19173; update patient_program set voided = true where patient_program.patient_program_id = 19174; update patient_program set voided = true where patient_program.patient_program_id = 19195; update patient_program set voided = true where patient_program.patient_id in (10407, 10417, 10438, 10446, 10459, 10458); update person set voided = true where person.person_id = 7634; update person set voided = true where person.person_id in (3386, 5021, 10160, 10278, 10440, 10488); update encounter set encounter.voided = true where encounter.encounter_id in (369280, 383732, 387915);

update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (select min(e.encounter_id) id from encounter e where e.voided = false

and e.encounter_type = 18

group by e.patient_id, e.encounter_datetime having count(*) > 1) t); update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (select min(e.encounter_id) id from encounter e where e.voided = false

and e.encounter_type = 18

group by e.patient_id, e.encounter_datetime having count(*) > 1) t);

update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (select distinct encounter.encounter_id id from encounter join obs on (obs.encounter_id = encounter.encounter_id) where encounter.voided = false and obs.voided = false and encounter.encounter_type = 18 and obs.concept_id = 5096 and encounter.encounter_datetime >= obs.value_datetime ) t);

update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (select min(encounter.encounter_id) id from encounter where encounter.voided = false and encounter.encounter_type in (5, 7) group by encounter.patient_id, encounter.encounter_datetime having count(*) > 1 ) t);

update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (select min(encounter.encounter_id) id from encounter where encounter.voided = false and encounter.encounter_type in (6, 9) group by encounter.patient_id, encounter.encounter_datetime having count(*) > 1 ) t);

update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (SELECT min(e.encounter_id) id FROM openmrs.encounter e

INNER JOIN openmrs.obs o ON e.encounter_id=o.encounter_id 

WHERE e.encounter_type IN (6,9) AND o.concept_id in (1113)
AND o.voided=0 and e.voided = false group by e.patient_id, o.value_datetime having count(*) > 1 ) t);

update encounter set encounter.voided = true where encounter.encounter_id in ( select id from (SELECT min(e.encounter_id) id FROM openmrs.encounter e INNER JOIN openmrs.obs o ON e.encounter_id=o.encounter_id WHERE e.encounter_type IN (6,9) AND o.concept_id=6120 AND o.voided=0 AND e.voided=0 group by e.patient_id having count(*) > 1 ) t);