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Error "Subscript out of bounds" when login to the EpiFlu and EpiRSV #54

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augauga opened this issue May 10, 2024 · 4 comments
Open

Error "Subscript out of bounds" when login to the EpiFlu and EpiRSV #54

augauga opened this issue May 10, 2024 · 4 comments

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@augauga
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augauga commented May 10, 2024

Hi! I encountered the following error when accessing the EpiFlu database:

> devtools::install_github("Wytamma/GISAIDR",ref = "EpiFlu")
> library(GISAIDR)
> credentials <- login(username = username, password = password, database="EpiFlu")
Error in matches[[1]][[2]] : subscript out of bounds

Besides, are there any other ways to access the EpiFlu database?
@Wytamma
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Wytamma commented May 12, 2024

Hey @augauga,

I’m working on epiflu access in a separate branch you’ll have to clone the repo and checkout that branch for experimental epiflu features. More details here -> #31 (comment)

-W

@Wytamma
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Wytamma commented May 12, 2024

Actually I see you did use the brach in your install step… Can you try turning on debug? Sys.setenv(GISAIDR_DEBUG = 1)

@augauga
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augauga commented May 13, 2024

Thank you for your reply! The debug message is as follow:

> Sys.setenv(GISAIDR_DEBUG = 1)
> credentials <- login(username = my_username, password = my_password, database="EpiFlu")
Sending request:
 Method -> GET
 URL -> https://www.epicov.org/epi3/frontend?
 data -> 
Extracting 'name="sid" value='([^']*)' from '
        <html>

        <body'
Sending request:
 Method -> GET
 URL -> https://www.epicov.org/epi3/frontend?sid=D9CE47ZQLWJT5NTIHRYGFKOIPS5JF2SR
 data -> 
Extracting '"WID"] = "([^"]*)' from '<!DOCTYPE html PUBLIC "-//W3C/'
Extracting 'PID"] = "([^"]*)' from '<!DOCTYPE html PUBLIC "-//W3C/'
Extracting 'sys.getC\('(.*)').call\('doLogin'' from '<!DOCTYPE html PUBLIC "-//W3C/'
Sending request:
 Method -> POST
 URL -> https://www.epicov.org/epi3/frontend?
 data -> sid=D9CE47ZQLWJT5NTIHRYGFKOIPS5JF2SR&wid=wid_sd2kf1_iumm&pid=pid_sd2kf1_iumn&data=%7B%22queue%22%3A%5B%7B%22wid%22%3A%22wid_sd2kf1_iumm%22%2C%22pid%22%3A%22pid_sd2kf1_iumn%22%2C%22cid%22%3A%22c_sd2kf1_74%22%2C%22cmd%22%3A%22doLogin%22%2C%22params%22%3A%7B%22login%22%3A%22cwn5810%22%2C%22hash%22%3A%22d88840057f69601e868ea106dc2ff64e%22%7D%2C%22equiv%22%3Anull%7D%5D%7D&ts=1715564396000&mode=ajax
Extracting '\('(.*)')' from 'sys.goPage('pid_sd2kf1_iumo')'
Sending request:
 Method -> GET
 URL -> https://www.epicov.org/epi3/frontend?sid=D9CE47ZQLWJT5NTIHRYGFKOIPS5JF2SR&pid=pid_sd2kf1_iumo
 data -> 
Extracting 'sys.call\('(.{5,20})','Go'' from '<!DOCTYPE html PUBLIC "-//W3C/'
Extracting ''_sid':'(.{30,100})','back'' from '<!DOCTYPE html PUBLIC "-//W3C/'
Extracting ''back':'(.{140,150})',' from '<!DOCTYPE html PUBLIC "-//W3C/'
Sending request:
 Method -> POST
 URL -> https://www.epicov.org/epi3/frontend?
 data -> sid=D9CE47ZQLWJT5NTIHRYGFKOIPS5JF2SR&wid=wid_sd2kf1_iumm&pid=pid_sd2kf1_iumo&data=%7B%22queue%22%3A%5B%7B%22wid%22%3A%22wid_sd2kf1_iumm%22%2C%22pid%22%3A%22pid_sd2kf1_iumo%22%2C%22cid%22%3A%22c_sd2kf1_zl%22%2C%22cmd%22%3A%22GoCloud%22%2C%22params%22%3A%7B%22cms_page%22%3A%22epi3%22%2C%22_sid%22%3A%2296F391ADOWJXWY9ABUIZ09VD0G05R709%22%2C%22back%22%3A%22eyJzaWQiOiAiRDlDRTQ3WlFMV0pUNU5USUhSWUdGS09JUFM1SkYyU1IiLCAibW9kZSI6ICJwYWdlIiwgIl91cmwiOiAiaHR0cHM6Ly93d3cuZXBpY292Lm9yZy9lcGkzL2Zyb250ZW5kIn0%3D%22%2C%22mode%22%3A%22page%22%2C%22_url%22%3A%22https%3A%2F%2Fplatform.epicov.org%2Fepi3%2Fcfrontend%22%7D%2C%22equiv%22%3Anull%7D%5D%7D&ts=1715564398000&mode=ajax
Sending request:
 Method -> POST
 URL -> https://platform.epicov.org/epi3/cfrontend?
 data -> cms_page=epi3&sid=96F391ADOWJXWY9ABUIZ09VD0G05R709&mode=page
Extracting 'pid_(.{5,15})"' from 'An internal server error occur'
Error in matches[[1]][[2]] : subscript out of bounds

@Wytamma
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Wytamma commented May 25, 2024

Hey @augauga, Can you confirm you have access to EpiFlu on gisaid.org (https://platform.epicov.org/epi3/frontend) and your search interface looks like this?

image

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@Wytamma @augauga