MLW-1722 - Migrate omrs_patient and mw_patient off of Pentaho

datasources/lowerNenoOpenmrs.yml

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+databaseType: "mysql"
+host: ${lowerNenoOpenmrs.host}
+port: ${lowerNenoOpenmrs.port}
+databaseName: ${lowerNenoOpenmrs.databaseName}
+user: ${lowerNenoOpenmrs.user}
+password: ${lowerNenoOpenmrs.password}
+options: ${lowerNenoOpenmrs.options}

datasources/upperNenoOpenmrs.yml

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+databaseType: "mysql"
+host: ${upperNenoOpenmrs.host}
+port: ${upperNenoOpenmrs.port}
+databaseName: ${upperNenoOpenmrs.databaseName}
+user: ${upperNenoOpenmrs.user}
+password: ${upperNenoOpenmrs.password}
+options: ${upperNenoOpenmrs.options}

jobs/create-source-views-and-functions.yml

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+type: "job-pipeline"
+description: "Load from SQL from ${sourceDatasource}"
+configuration:
+  jobs:
+    - type: "sql-execution"
+      description: "Create functions for ${sourceDatasource}"
+      configuration:
+        datasource: "${sourceDatasource}.yml"
+        delimiter: "#"
+        scripts:
+          - "sql/functions/person_address_city_village.sql"
+          - "sql/functions/person_address_county_district.sql"
+          - "sql/functions/person_address_state_province.sql"
+          - "sql/functions/person_family_name.sql"
+          - "sql/functions/person_given_name.sql"
+          - "sql/functions/person_name.sql"
+          - "sql/functions/person_phone_number.sql"

jobs/sql-extract-and-transfer-to-table.yml

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+# Template that takes in the following parameters
+# ${tableName}
+# ${sourceDatasource}
+# ${targetDatasource}
+type: "sql-transfer"
+description: "Extracting from ${sourceDatasource} to ${tableName} in ${targetDatasource}"
+configuration:
+  extract:
+    datasource: "${sourceDatasource}.yml"
+    query:  "sql/extractions/${tableName}.sql"
+  load:
+    datasource: "${targetDatasource}.yml"
+    table: "${tableName}"
+    schema: "sql/schemas/${tableName}.sql"
+    bulkCopy:
+      batchSize: 400

jobs/sql/extractions/mw_patient_2.sql

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+drop temporary table if exists temp_patient;
+create temporary table temp_patient (
+  patient_id            INT NOT NULL PRIMARY KEY,
+  patient_uuid	 	    CHAR(38),
+  first_name            VARCHAR(50),
+  last_name             VARCHAR(50),
+  gender                CHAR(1),
+  birthdate             DATE,
+  birthdate_estimated   BOOLEAN,
+  phone_number          VARCHAR(50),
+  district              VARCHAR(255),
+  traditional_authority VARCHAR(255),
+  village               VARCHAR(255),
+  chw_person_id         INT,
+  chw                   VARCHAR(100),
+  dead                  BOOLEAN,
+  death_date            DATE
+);
+
+insert into temp_patient (patient_id, patient_uuid, gender, birthdate, birthdate_estimated, dead, death_date)
+select      n.person_id as patient_id,
+            n.uuid as patient_uuid,
+            n.gender,
+            n.birthdate,
+            n.birthdate_estimated,
+            n.dead,
+            n.death_date
+from        patient p
+inner join  person n on p.patient_id = n.person_id
+where       p.voided = 0
+  and       n.voided = 0
+;
+
+update temp_patient set first_name = person_given_name(patient_id);
+update temp_patient set last_name = person_family_name(patient_id);
+update temp_patient set phone_number = phone_number(patient_id);
+update temp_patient set district = person_address_state_province(patient_id);
+update temp_patient set traditional_authority = person_address_county_district(patient_id);
+update temp_patient set village = person_address_city_village(patient_id);
+
+select relationship_type_id into @chwRelationshipType from relationship_type where a_is_to_b = 'Community Health Worker';
+
+update temp_patient p set chw_person_id = (
+    select r.person_a
+    from relationship r
+    where r.person_b = p.patient_id
+    and r.voided = 0
+    and r.relationship = @chwRelationshipType
+    order by if(r.end_date is null, 1, 0) desc, if(r.start_date is null, 0, 1) desc, r.date_created desc
+    limit 1
+);
+
+update temp_patient set chw = person_name(chw_person_id);
+
+select
+    patient_id,
+    patient_uuid,
+    first_name,
+    last_name,
+    gender,
+    birthdate,
+    birthdate_estimated,
+    phone_number,
+    district,
+    traditional_authority,
+    village,
+    chw,
+    dead,
+    death_date
+from temp_patient;

jobs/sql/functions/person_address_city_village.sql

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+#
+DROP FUNCTION IF EXISTS person_address_city_village;
+#
+CREATE FUNCTION person_address_city_village(
+    _person_id int
+)
+	RETURNS TEXT
+    DETERMINISTIC
+
+BEGIN
+    DECLARE patientAddressCityVillage TEXT;
+
+	select city_village into patientAddressCityVillage
+    from person_address where voided = 0 and person_id = _person_id order by preferred desc, date_created desc limit 1;
+
+    RETURN patientAddressCityVillage;
+
+END
+#

jobs/sql/functions/person_address_county_district.sql

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+#
+DROP FUNCTION IF EXISTS person_address_county_district;
+#
+CREATE FUNCTION person_address_county_district(
+    _person_id int
+)
+    RETURNS TEXT
+    DETERMINISTIC
+
+BEGIN
+    DECLARE personAddressCountyDistrict TEXT;
+
+    select county_district into personAddressCountyDistrict
+    from person_address where voided = 0 and person_id =  _person_id order by preferred desc, date_created desc limit 1;
+
+    RETURN personAddressCountyDistrict;
+
+END
+#

jobs/sql/functions/person_address_state_province.sql

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+#
+DROP FUNCTION IF EXISTS person_address_state_province;
+#
+CREATE FUNCTION person_address_state_province(
+    _person_id int
+)
+    RETURNS TEXT
+    DETERMINISTIC
+
+BEGIN
+    DECLARE patientAddressStateProvince TEXT;
+
+    select state_province into patientAddressStateProvince
+    from person_address where voided = 0 and person_id = _person_id order by preferred desc, date_created desc limit 1;
+
+    RETURN patientAddressStateProvince;
+
+END
+#

jobs/sql/functions/person_family_name.sql

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+#
+DROP FUNCTION IF EXISTS person_family_name;
+#
+CREATE FUNCTION person_family_name(
+    _person_id int
+)
+    RETURNS TEXT
+    DETERMINISTIC
+
+BEGIN
+    DECLARE personFamilyName TEXT;
+
+    select      family_name into personFamilyName
+    from        person_name
+    where       voided = 0
+      and         person_id = _person_id
+    order by    preferred desc, date_created desc
+    limit       1;
+
+    RETURN personFamilyName;
+
+END
+#

jobs/sql/functions/person_given_name.sql

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+#
+DROP FUNCTION IF EXISTS person_given_name;
+#
+CREATE FUNCTION person_given_name(
+    _person_id int
+)
+    RETURNS TEXT
+    DETERMINISTIC
+
+BEGIN
+    DECLARE personGivenName TEXT;
+
+    select      given_name into personGivenName
+    from        person_name
+    where       voided = 0
+      and         person_id = _person_id
+    order by    preferred desc, date_created desc
+    limit       1;
+
+    RETURN personGivenName;
+
+END
+#

jobs/sql/functions/person_name.sql

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+#
+DROP FUNCTION IF EXISTS person_name;
+#
+CREATE FUNCTION person_name(
+    _person_id int
+)
+    RETURNS TEXT
+    DETERMINISTIC
+
+BEGIN
+    DECLARE personName TEXT;
+
+    select      concat(given_name, ' ', family_name) into personName
+    from        person_name
+    where       voided = 0
+      and       person_id = _person_id
+    order by    preferred desc, date_created desc
+    limit       1;
+
+    RETURN personName;
+
+END
+#

jobs/sql/functions/person_phone_number.sql

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+#
+DROP FUNCTION IF EXISTS phone_number;
+#
+CREATE FUNCTION phone_number(
+    _person_id int)
+
+    RETURNS VARCHAR(50)
+    DETERMINISTIC
+
+BEGIN
+    DECLARE  attVal VARCHAR(50);
+
+    select      a.value into attVal
+    from        person_attribute a
+    inner join  person_attribute_type t on a.person_attribute_type_id = t.person_attribute_type_id
+    where       t.name = 'Cell Phone Number'
+    and         a.voided = 0
+    and         a.person_id = _person_id
+    order by    a.date_created desc
+    limit       1;
+
+    RETURN attVal;
+
+END
+#

jobs/sql/schemas/mw_patient_2.sql

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+CREATE TABLE mw_patient_2 (
+    patient_id            INT NOT NULL PRIMARY KEY,
+    patient_uuid	 	  CHAR(38),
+    first_name            VARCHAR(50),
+    last_name             VARCHAR(50),
+    gender                CHAR(1),
+    birthdate             DATE,
+    birthdate_estimated   BOOLEAN,
+    phone_number          VARCHAR(50),
+    district              VARCHAR(255),
+    traditional_authority VARCHAR(255),
+    village               VARCHAR(255),
+    chw                   VARCHAR(100),
+    dead                  BOOLEAN,
+    death_date            DATE
+);

jobs/test.yml

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+type: "job-pipeline"
+description: "Refreshing Upper Neno data"
+parameters:
+  sourceDatasource: "upperNenoOpenmrs"
+  targetDatasource: "upperNenoReporting"
+configuration:
+  jobs:
+    - path: "create-source-views-and-functions.yml"
+    - type: "iterating-job"
+      description: "Extracting from ${sourceDatasource} to ${tableName} in ${targetDatasource}"
+      configuration:
+        maxConcurrentJobs: 1
+        jobTemplate:
+          path: "sql-extract-and-transfer-to-table.yml"
+        iterations:
+          - tableName: "mw_patient_2"