MIT-LCP / MIT-LCP/mimic-code

Error loading MIMIC-IV 3.0 with the V 2.2 postgres create.sql script

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Description

Prerequisites
Description

Description of the issue, including:

  • The admissions.csv in version 3.0 has values for too long for the 'language' column. This causes the load.sql script to fail:
  • SET
    psql:load.sql:16: ERROR: value too long for type character varying(10)
    CONTEXT: COPY admissions, line 238, column language: "Kabuverdianu"
    and later with
    psql:load_admissions.sql:16: ERROR: value too long for type character varying(12)
    CONTEXT: COPY admissions, line 387, column language: "American Sign Language"

I fixed it by changing the 'language' column VARCHAR limit to 30. This will surely be fixed if and when a 3.0 version of code is released.

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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 with the PostgreSQL schema in the v2.2 create.sql script and the loading steps in load.sql and load_admissions.sql. Reproduce the MIMIC-IV 3.0 admissions import using the reported language values, then verify that the schema accepts the data without COPY errors. Done means the documented load completes successfully with the affected language values.

Written by the indexing model from the issue text.

Assessment

Tech stack
postgresql, sql
Domain
databases
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
65/100

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