Entering edit mode
I'm trying to update my local snapshot of the ENCODE database to use with ENCODExplorer, however I get a 404 error. Any suggestions?
tables = prepare_ENCODEdb(database_filename)
[1] "Tue Mar 01 09:55:07 2016"
Error in open.connection(con, "rb") : HTTP error 404.
> traceback()
10: open.connection(con, "rb")
9: open(con, "rb")
8: parse_con(txt, 1024^2, bigint_as_char)
7: parseJSON(txt, bigint_as_char)
6: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame,
simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
5: jsonlite::fromJSON(url)
4: extract_table(type)
3: FUN(X[[i]], ...)
2: lapply(types, extract_type)
1: prepare_ENCODEdb(database_filename)
Edit: this works on my (Mac) laptop - it doesn't work on my colleague's laptop running ArchLinux, or on our server running Debian, or on Fedora.
I've also tracked down that the url it's trying to access when it fails is https://www.encodeproject.org/search/?type=access_key&limit=all&frame=object&format=json.
This isn't very helpful, but it worked just now for me:
> prepare_ENCODEdb("/tmp/encode.sql") [1] "Tue Mar 01 01:41:21 PM 2016" [1] "Extract the tables from the ENCODE rest api : 12.3562210559845 min"Maybe the connection is just a bit flaky?
Oh, it works for me now on my laptop but not on our group's server. So I can just copy over the sqlite file. Maybe it's a problem with the server then.