ETL birth mother registry is done. All tests PASS.

[shanmukhasampath]

This is for issue #120

Birth Mother registry ETL is finished.

1. Added necessary setup functions for birth mother registry without disturbing other registries
2. Changed TestFramework.R to be able to do unittests.
3. SQL scripts to run ETL of birth mother registry data
4. Test scripts in R for unit testing
5. Changed input DEATH registry to death_registry which makes the unit tests work properly

[javier-gracia-tabuenca-tuni]

id like to see config/run_config_template.R

[javier-gracia-tabuenca-tuni]

from slack

what if we put all the unittest_etl_birthmother* files into one file unittest_etl_birth_mother_event_tables.R ?? 2:31 and we have it in "birth_mother stem_medical_events" , here::here("sql/etl_birth_mother_stem_medical_events.sql"), "unittest_etl_birth_mother_event_tables.R", TRUE, TRUE,

[shanmukhasampath]

Combined birth mother unit tests for condition, procedure, observation and measurement tables into one file.

Should the run_config_template.R also be updated?

[javier-gracia-tabuenca-tuni]

add an offset to the visit_occurrence_id, to make it independent of the size of other registers for example 1 000 000 000 000 + mother visit I guess in finregister is not gonnabe more than 1B visits ?

[shanmukhasampath]

Fixed the visit_occurrence table for birth mother with offset.

[shanmukhasampath]

Birth mother visit and stem medical events are ready to be published. Initial versions takes care of the following scenarios

• Twins should have same APPROX_BIRTH_DATE but due to the way the data is setup we have different dates for twins delivered and gap range either 6 or 11 or 14 or <30 days. To overcome this we are currently using APPROX_DELIVERY_DATE = MOTHER APPROX_BIRTH_DATE (from finngenid_info) + MOTHER_AGE (from birth_mother)
• Not every birth event in the birth_mother registry has at least one DIAGNOSIS column not NULL. To overcome this, we add a default value of Z37 ICD10fi code meaning OUTCOME OF DELIVERY for all birth events in birth_mother registry.

Improvements will be followed in another issue.