Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

NumberFormatException allows "Unknown" for month day and year but inputing this gives SRA error #35

Open
jdeck88 opened this issue Jul 1, 2020 · 0 comments

Comments

@jdeck88
Copy link
Member

jdeck88 commented Jul 1, 2020

Downloading SRA data with month or day of "Unknown" gives an error. However, the SRA downloader will give an error:

java.lang.NumberFormatException: For input string: "Unknown"
	at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.base/java.lang.Integer.parseInt(Integer.java:652)
	at java.base/java.lang.Integer.parseInt(Integer.java:770)
	at biocode.fims.geome.sra.GeomeBioSampleMapper.getCollectionDate(GeomeBioSampleMapper.java:242)
	at biocode.fims.geome.sra.GeomeBioSampleMapper.recordToBioSample(GeomeBioSampleMapper.java:171)

This returns a server error to interface. I think we enabled "Unknown" for the Number Format rule for years for cases where this value is not known. I need to research the root of the error when downloading SRA data and see if we should just translate Unknown values to null values (could work) and/or if these values are actually required. In any case, we should only allow "Unknown" as a value for Year since it is a GEOME required field. For projects that actually want to be more explicit in requiring month and day we should not allow unknown values.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant