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outbreak-info / R-outbreak-info

R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.
https://outbreak-info.github.io/R-outbreak-info/
MIT License
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Issues with GetPrevalence() when seraching for ONLY mutations #104

Closed TKMarkCheng closed 1 year ago

TKMarkCheng commented 1 year ago

GetPrevalence() returns Malformed Token Error. The example search of E484K within getPrevalence.R returns the following error.

> E484K_prevalence = getPrevalence(mutation = c("S:E484K"))
Retrieving data... 
Warning: Malformed token. Please reauthenticate by calling the authenticateUser() function.
Error in invokeRestart("muffleWarning") : 
  no 'restart' 'muffleWarning' found

Adding a search pangolin_lineage rescues this behavior (i.e. getPrevalence(pangolin_lineage = "P.1", mutation = c("S:E484K")), but 1) Searching for multiple mutations; or 2) adding a location does not fix the issue.

pengwei1993 commented 1 year ago

so how solve this problem? If I want to search for E484K mutation from all lineages rather than one lineage

pengwei1993 commented 1 year ago

so how solve this problem? If I want to search for E484K mutation from all lineages rather than one lineage

one month ago, I can search for E484K mutation from all lineages,now It's wrong

TKMarkCheng commented 1 year ago

@flaneuse this is a relatively debilitating error for the genomics API, and it seems to be a problem on the outbreak.info website itself as well. I'm gusesing this is a sever or an API problem?

pengwei1993 commented 1 year ago

您好，来信已收到，我会尽快回复。 尽快给您回复。

flaneuse commented 1 year ago

@TKMarkCheng thanks for bringing this to our attention. you're correct: it was a parameter incorrectly set on the API. Fixed in https://github.com/outbreak-info/outbreak.api/pull/86

pengwei1993 commented 1 year ago

So? This problem could be solved?

TKMarkCheng commented 1 year ago

Thank you @flaneuse for your timely reply and the team for fixing the issue! @pengwei1993 it would be nice if you can be more courteous and more specific when raising issues on GitHub, but yes, the outbreak.info team has kindly fixed the issue as of today (18th March 2023).

E484K_prevalence = getPrevalence(mutation=c("S:E484K"))
E484K_prevalence
plotPrevalenceOverTime(E484K_prevalence)

yields the following figure. image

pengwei1993 commented 1 year ago

great, thank you

 

------------------ 原始邮件 ------------------ 发件人: "outbreak-info/R-outbreak-info" @.>; 发送时间: 2023年3月18日(星期六) 上午9:49 @.>; 抄送: "Li @.**@.>; 主题: Re: [outbreak-info/R-outbreak-info] Issues with GetPrevalence() when seraching for ONLY mutations (Issue #104)

Thank you @flaneuse for your timely reply and the team for fixing the issue! @pengwei1993 it would be nice if you can be more courteous and more specific when raising issues on GitHub, but yes, the outbreak.info team has kindly fixed the issue as of today (18th March 2023). E484K_prevalence = getPrevalence(mutation=c("S:E484K")) E484K_prevalence plotPrevalenceOverTime(E484K_prevalence)
yields the following figure.

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