Pevious MEDS ETL not running

[bnevesmd]

HI there. We are trying to convert our OMOP data to MEDS format in order to use CLMBR-T. We realize older version of MEDS 0.1.1 is required, however we are keeping having the following error when running meds_etl:

Generating metadata from OMOP concepttable 100%|█████████████████████████████████████████████| 1/1 [00:09<00:00, 9.29s/it] Finding birth and death codes: 92%|▉| 8340025/9093629 [00:02<00:00, 3410987.07i Decompressing OMOP tables, mapping to MEDS Flat format, writing to disk... 0%| | 0/6 [00:00<?, ?it/s]/anaconda/envs/embeddings/lib/python3.9/site-packages/meds_etl/omop.py:169: PerformanceWarning: Determining the column names of a LazyFrame requires resolving its schema, which is a potentially expensive operation. UseLazyFrame.collect_schema().names()to get the column names without this warning. pl.col(table_name + option) for option in options if table_name + option in batch.columns [/anaconda/envs/embeddings/lib/python3.9/site-packages/meds_etl/omop.py:196]: PerformanceWarning: Determining the column names of a LazyFrame requires resolving its schema, which is a potentially expensive operation. UseLazyFrame.collect_schema().names() to get the column names without this warning. if concept_id_field.replace("_concept_id", "_source_concept_id") in batch.columns: 0%| | 0/6 [00:03<?, ?it/s] Traceback (most recent call last): File "/anaconda/envs/embeddings/bin/meds_etl_omop", line 8, in <module> sys.exit(main()) File "/anaconda/envs/embeddings/lib/python3.9/site-packages/meds_etl/omop.py", line 704, in main process_table(task) File "/anaconda/envs/embeddings/lib/python3.9/site-packages/meds_etl/omop.py", line 216, in process_table code = concept_id.map_dict(concept_id_map) AttributeError: 'Expr' object has no attribute 'map_dict'

Thank you!

[EthanSteinberg]

Hi bnevesmd,

Can you try meds_etl == 0.1.3 instead of 0.1.1?

I think that should fix the issue you were facing. I'll get the documentation on our side updated to point to the right versions.