[BUG]: Server code: 503; Server is possibly experiencing traffic, trying again...

[Kiven668]

when I execute below codes, it returns 503. it worked a few days before. could you help on this? thank you.

id_exposure <- c("ieu-b-4846", "ieu-b-4850", "met-d-ApoB", "met-d-Total_C", "ukb-a-290" )
library(TwoSampleMR)
options(ieugwasr_api = 'gwas-api.mrcieu.ac.uk/')
#options(ieugwasr_api = 'https://api.opengwas.io/api')
exposure_dat <- mv_extract_exposures(id_exposure,
                                       opengwas_jwt = "<my jwt>")  

[JasonQiu]

Please remove both options() lines, save the code, restart session and try again.

options() can be used to toggle the API base URL, however it should not be used by end users unless instructed by the docs or a member of our team. If you are using the latest versions of TwoSampleMR and ieugwasr then https://api.opengwas.io/api will be the default value and there is no need to set/alter that.

We understand there are comments posted somewhere during the transitional period, suggesting that altering the base URL to gwas-api.mrcieu.ac.uk (the old service) could be helpful. In fact that will not work anymore because it is being decommissioned now and we are only able to provide support to those who are using api.opengwas.io/api (the new service).

Users may argue that gwas-api.mrcieu.ac.uk still works intermittently, however we would like to emphasise that it is not maintained anymore.

[Kiven668]

@JasonQiu thank you for your quick response. I removed both options but it returned another error. I remember I resolve this issue by add the option before. could you help on this?
Error in if (nrow(d) == 0) return(NULL) : argument is of length zero

[JasonQiu]

@JasonQiu thank you for your quick response. I removed both options but it returned another error. I remember I resolve this issue by add the option before. could you help on this? Error in if (nrow(d) == 0) return(NULL) : argument is of length zero

@Kiven668 Please provide full, minimal and reproducible example (code and data). Assume I have installed the latest versions of TwoSampleMR and ieugwasr but know nothing about your work, please help me reproduce the error.

[Kiven668]

@JasonQiu the code is as below.

id_exposure <- c("ieu-b-4846", "ieu-b-4850", "met-d-ApoB", "met-d-Total_C", "ukb-a-290" )
library(TwoSampleMR)
exposure_dat <- mv_extract_exposures(id_exposure,
                                       opengwas_jwt = "<my jwt>")  

[JasonQiu]

Follow the steps exactly as shown here (in step 6, if user() is not working, try ieugwasr::user()):
https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication

In your code, remove the opengwas_jwt parameter from mv_extract_exposures() and all other similar functions. This parameter is not required if you have followed the instructions above carefully and set up OPENGWAS_JWT in .Renviron. https://mrcieu.github.io/TwoSampleMR/reference/mv_extract_exposures.html#arg-opengwas-jwt

[Kiven668]

@JasonQiu where is the .Renviron file? shall I create it somewhere?

[remlapmot]

The .Renviron file is just a text file you create in either your home directory or the working directory of your project. Most people have one in their home directory.

The easiest way to create one from inside R is to use the function in the usethis package as follows

install.packages("usethis")
usethis::edit_r_environ()

After you have saved the edits to the file (i.e., included your token on a line with OPENGWAS_JWT=) you then need to close and restart R/RStudio.