MIT-LCP / MIT-LCP/mimic-code

tables seem to be created and compressed files loaded (step 6) but dataset dos not seem to be working (step 7)

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Description

Prerequisites

I am stuck at the last two steps in uploading and creating datasets in google chloud.
https://github.com/MIT-LCP/mimic-iv/tree/master/buildmimic/bigquery

step 6 seemed to work

  • I was able to reproduce the full anticipated output. (see 1st screenshot)

step 7 was not successful

  • yielding the following error message: BigQuery error in query operation: Error processing job 'mimic-iv-20:bqjob_r690dd45440abac93_0000018aa1f66233_1': Not found: Table mimic-iv-20:mimic4_v1_0.patients was not found in location US (see 2nd screenshot)
  • I checked that the location of my dataset is indeed in the US (see 3rd screenshot)

How can I proceed to create the dataset?

  • I also verified on google cloud that there was indeed no tables created within the dataset mimic4_v1_0. (see 4th screenshot)

1st screenshot. upload_mimic4_v1_0.sh seemed to work
image

2nd screenshot. table not found; unable to validate dataset works
image

3rd screenshot. location of dataset is in US
image

4th screenshot. dataset indeed does not contain the anticipated/required tables
image

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in buildmimic/bigquery, especially upload_mimic4_v1_0.sh and the commands for steps 6 and 7. Compare the successful upload output with the failing dataset-creation query and verify the project, dataset, table names, and US location. Done means the expected tables, including patients, exist and step 7 completes successfully.

Written by the indexing model from the issue text.

Assessment

Tech stack
google-cloud, shell
Domain
cloud, databases
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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