Closed kuanyili closed 8 months ago
Thanks for letting us know. The data will be updated in the next release.
What you get via the API is real time.
Whenever we release we update the data as well, so what you're seeing now is a snapshot of what was available at release.
What you get via the API is real time.
Whenever we release we update the data as well, so what you're seeing now is a snapshot of what was available at release.
This was also what I thought, but I checked cpic_db_dump-v1.35.0.sql.gz
, which was released on Dec. 19, 2023. The ≥3.75
annotation was there, and the JSON stated that it uses CPIC version v1.35. Am I missing something?
@markwoon There was a mismatch between DB's that caused what's in the CPIC DB to not match what was pulled in DataManager. We can talk specifics later, but I will fix this immediate problem in the next release.
The fix has been pushed into development branch and will be in the next release.
Thank you for the support! 😄
@whaleyr @markwoon Hi! This issue kind of resurfaced since commit a57b955b3f42e0786154093a437e74393f89b4c0. Any idea?
Looking into it, thanks for pointing it out.
We changed how we handle diplotype data so must have re-introduced a bug.
Found the problem and pushed an updated phenotype file in cae0f8c6da998b0abc5ca2fc78aa7fa69767d600 that should address this issue.
Cool! Many thanks!
More specifically, diplotypes
*1x≥3/*41x3
*2x≥3/*41x3
currently have
in
src/main/resources/org/pharmgkb/pharmcat/phenotype/cpic/CYP2D6.json
.But instead they shall have
according to
curl --silent 'https://api.cpicpgx.org/v1/diplotype?genesymbol=eq.CYP2D6&diplotype=eq.*1x≥3/*41x3'
curl --silent 'https://api.cpicpgx.org/v1/diplotype?genesymbol=eq.CYP2D6&diplotype=eq.*2x≥3/*41x3'
Activity score
≥3.75
is also consequently missing indocs/Phenotypes-List.md
.Is the JSON data resource generated by a program so I should start from there to ensure future correctness? Or is the file maintained manually so I can just submit a PR by directly editing the file?