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
- Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.mit.edu/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
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
2nd screenshot. table not found; unable to validate dataset works
3rd screenshot. location of dataset is in US
4th screenshot. dataset indeed does not contain the anticipated/required tables
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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