VEuPathDB / VEuPathDB/study-wrangler
Validation should detect problems with very small numbers not working in EDA Number vars
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- Dominant language
- R
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- 0
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- 0
- Avg merge
- 2d 1h
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Description
The problem is due to Oracle storing the number_value column in AttributeValue tables as NUMBER which has a limit of 38 digits of precision. Thus anything smaller than 1e-38 will be a problem. p-values are commonly smaller than this.
This may not be a problem in Postgres if we use NUMERIC as the type?
Contributor guide
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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
Begin by locating validation for EDA Number variables and the AttributeValue.number_value storage definition. Compare the Oracle NUMBER precision described in the issue with PostgreSQL NUMERIC behavior; the work is complete when values smaller than 1e-38 are reliably identified as problematic.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- postgresql, r
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100