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OHDSI / MIMIC

MIMIC (Medical Information Mart for Intensive Care) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. This repository contains the ETL to the OMOP CDM.
Apache License 2.0
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Google Cloud Configuration Instructions #10

Open ruppert20 opened 3 years ago

ruppert20 commented 3 years ago

Is there a Readme for configuring the google cloud projects and datasets to run the ETL? I am getting the following error:

"BigQuery error in query operation: Error processing job 'mimic-omop:bqjob_r433fa0779e4406df_000001776a2fcc2e_1': Not found: Table mimic-omop:mimic_full_cdm.src_transfers was not found in location US".

I am not sure if this is relating to a configuration issue on my end or if the script was supposed to create the src_transfers table first.

Any help would be appreciated. Thank you for your time.

mik-ohdsi commented 3 years ago

Hi Matthew (@ruppert20), apologies for not getting back to you earlier. The project is not yet completely finalized and the documentation for the ETL is still not uploaded here. The MIMIC tables that the ETL starts from all receive a 'src_' prefix for the current ETL logic to run. Then the data and mappings are loaded into lookup tables before the actual transfer and load logic creates OMOP CDM data from them. Please bear with us a little longer while we are trying to close and finalize this project.

mik-ohdsi commented 3 years ago

Hi @ruppert20 m, as Tomer has pointed out in #11 there is a possibility that this also has to do with the location setting. We should try to make this more international so that you can control the GCP location setting in the configuration file. Other than that, stay tuned for more documentation here.