OHDSI/MIMIC

How to find tmp_concept data file?

Opened this issue · 2 comments

I have an error in vocabulary_refresh.py step 12~13
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I can't find any tmp_concept data file anywhere.
Please help for me.

Also, I have extra question. I had a json file in bigquery for schema.
I set gs_file_path ext for .json and saved in bigquery. But, I had an error like this.
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How can I solve the problem?

Hey @Kisooofficial - for the first problem: the tmp_concept table is created to overcome a problem on date format conversion during import. For some of the tables you have to create temporary tables with string fields for the date to which you import the vocabulary data. Then, in a second step you fill the actual final tables by using the above query that parses the date field content properly.
for the second problem: This is pretty hard to trouble-shoot without knowing your domain.json or relationship.json file. Where are these from? ETL-Synthea? One possible ddl logic can be found here.

Hello, This problem had already been resolved too. Thank you for comment.