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Empty tables after ETL-Synthea when using recent vocabulary download


(Mark Miller) #1

I am extremely appreciative of the OMOP ETL scripts on GitHub. Specifically, I have received some helpful replies to issues I’ve posted on the Synthea ETL repository https://github.com/OHDSI/ETL-Synthea

Having said that, I’ve never been able to get it to run without some kind of modification. (I’m using Postgres 11 on Ubuntu 18). I pulled the ETL code and the vocabularies today, and the ETL ran to completion, but some of the patient-level CDM tables weren’t populated.


Update: there may be something wrong with the vocabularies I pulled today. There weren’t any rows with target_vocabulary_id = ‘SNOMED’ in source_to_standard_vocab_map (only ‘CPT4’). Maybe I did something wrong in the CPT download from UMLS.

Here’s a log of the ETL that wasn’t completely successful when I used my most recent vocabulary download. See also https://github.com/OHDSI/ETL-Synthea/issues/28

Performing ETL
Loading person
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 1189
Loading observation_period
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 1189
Loading visit_occurrence
INSERT 0 36985
Loading observation
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 0
Loading condition_occurrence
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 8750
Loading procedure_occurrence
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 0
Loading measurement
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 0
Loading drug exposure
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 0
Loading condition_era
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 7132
Loading drug_era
DROP SEQUENCE
CREATE SEQUENCE
INSERT 0 0

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