Closed woaidangyang closed 2 years ago
Hi @woaidangyang,
Thanks for checking out the package! Sorry for the late reply, I was on vacation. In theory you should be able to do this if you place it in the /cache/
folder for OmniPath, but the download should work anyways. @deeenes what could be happening here?
Hi,
The issue above most likely means that your curl
R package was compiled against an old curl
library or libressl
library, or the operating system's certificate store needs an update, or there is a firewall which interferes with the connection. To know more about the reasons, you can run curl
in verbose mode:
library(curl)
library(httr)
# see some details about your curl:
curl_version()
# see the debug trace of this connection:
progeny_url <- 'https://omnipathdb.org/annotations?resources=PROGENy&license=academic'
p <- GET(progeny_url, verbose(data_in = TRUE, info = TRUE, ssl = TRUE))
Also you can try to update the curl
R package, it might help, especially if you also update the libcurl
and libressl
used for the compilation.
To manually insert cache content as Pau suggested, you can extract the attached zip into the cache directory of OmnipathR, and add this to the cache.json
file in the directory, with modifying the path /home/...
to your actual cache directory:
{
...
"3492392585ba05414edfae46801492076437d7e7": {
"key": ["3492392585ba05414edfae46801492076437d7e7"],
"url": ["https://omnipathdb.org/annotations?resources=PROGENy&license=academic"],
"post": [],
"payload": [],
"ext": ["rds"],
"versions": {
"1": {
"number": ["1"],
"path": ["/home/denes/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds"],
"dl_started": ["2022-05-18 20:37:10"],
"status": ["ready"],
"dl_finished": ["2022-05-18 20:37:12"]
}
}
},
...
}
To find the cache directory:
library(OmnipathR)
OmnipathR:::omnipath_get_cachedir()
# [1] "/home/denes/.cache/OmnipathR"
While running
net <- get_progeny(organism = 'human', top = 100)
, I kept getting this error:But I have no problem downloading
https://omnipathdb.org/annotations?resources=PROGENy&license=academic
using the browser. I'd like to ask if you can add an option so we can just retrieve the data from the locally downloaded file.Thank you so much for your great work!