Empty icuid issue when execute mimic_direct_extract.py

[a11525]

Dear MIMIC_Extract team,

I have been following the step-by-step instructions in the MIMIC_extract readme to run the mimic_direct_extract.py script. However, I encountered an error at line 5: where c.icustay_id in (). The issue seems to be with the empty parentheses in in (), which is caused by the icuids variable being empty at line 888 (({icuids})) in the mimic_direct_extract.py script.

I noticed that there have been changes in the MIT-LCP Repo, where the postgres-function.sql file is no longer present in the concepts directory. Instead, I used the postgres-function.sql file from the following location: [https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iii/concepts_postgres]. Additionally, I used the postgres-make-concepts.sql file from the same repository.

I also used the convert_mimiciii_concepts_bq_to_psql.sh script from the concepts directory, executing it with bash.

Could you please guide me on what could be the possible issue and which parts I should check and modify to resolve this error?

Thank you for your assistance.

Best regards,
Sanghoon