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ohdsi-etl-prias's Issues

Using NAACCR

I see we use some mappings to NAACCR concepts, e.g. 35917476. This vocabulary is not by default included in a download from Athena (needs to be selected manually).

Is the use of NAACCR vocabularies documented somewhere? (both here and in the ohdsi-omop-pioneer repo).

Episode event domain lookup; better error if concept not found

The error below is thrown by wrapper.get_event_field_concept_id(concept_id) when the given concept_id cannot be found in the vocabulary. This actually indicates that the vocabulary has not been loaded correctly, but the error message is very cryptical AttributeError: 'NoneType' object has no attribute 'split'.

We should gracefully handle this exception by showing a simple warning message.

Please note that normally this would give an error in an earlier stage as the concept_id constraint do not hold for the earlier inserted (observation) record. I got below error when I removed the vocabulary constraints when running at the client who could not load the vocabs.

2020-05-12 10:45:50,386 - ERROR - No row was found for one()
2020-05-12 10:45:50,386 - INFO - Performing rollback
2020-05-12 10:45:50,389 - INFO - Rollback completed
2020-05-12 10:51:13,976 - ERROR - #!#! ERROR: Transformation 'basedata_to_episode_event' failed:
2020-05-12 10:51:13,981 - ERROR - Traceback (most recent call last):
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/model/EtlWrapper.py", line 217, in execute_transformation
    records_to_insert = statement(self)
AttributeError: 'NoneType' object has no attribute 'split'

2020-05-12 10:51:13,982 - ERROR - 'NoneType' object has no attribute 'split'
2020-05-12 10:51:13,982 - ERROR - ##### START FULL TRACEBACK #####
2020-05-12 10:51:13,984 - ERROR - 
Traceback (most recent call last):
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/model/EtlWrapper.py", line 217, in execute_transformation
    records_to_insert = statement(self)
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/transformation/basedata_to_episode_event.py", line 113, in basedata_to_episode_event
    event_field_concept_id = wrapper.get_event_field_concept_id(target.concept_id)
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/wrapper.py", line 321, in get_event_field_concept_id
    domain_prefix = domain_id.split('_')[0]
AttributeError: 'NoneType' object has no attribute 'split'
#Traceback (most recent call last):
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/model/EtlWrapper.py", line 217, in execute_transformation
    records_to_insert = statement(self)
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/transformation/basedata_to_episode_event.py", line 113, in basedata_to_episode_event
    event_field_concept_id = wrapper.get_event_field_concept_id(target.concept_id)
  File "/Users/Maxim/Develop/OHDSI/ohdsi-etl-prias/src/main/python/wrapper.py", line 321, in get_event_field_concept_id
    domain_prefix = domain_id.split('_')[0]
AttributeError: 'NoneType' object has no attribute 'split'

Update unit tests

Part of the current RiaH unit tests are not in sync with transformation logic.

Add database setup in ETL

Different from the erspc approach, Docker will not do the setup.
The ETL script should create target schema, vocabulary loading, add source daimon and run Achilles.

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