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April 10, 2019 17:33
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Issue with creating/updating network on NDEx
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# ndexr relies on httr but doesn't handle importing it | |
library(httr) | |
library(ndexr) | |
NDEX_USER <- Sys.getenv("NDEX_USER") | |
NDEX_PWD <- Sys.getenv("NDEX_PWD") | |
NETWORK_ID <- '37800bb2-5bb4-11e9-831d-0660b7976219' | |
ndexcon <- NA | |
if (NDEX_USER == '' || NDEX_PWD == '') { | |
message <- 'Error: environment variables NDEX_USER and/or NDEX_PWD not set.' | |
write(message, stderr()) | |
write('In your terminal, run:', stderr()) | |
write('export NDEX_USER=\'your-ndex-username\'', stderr()) | |
write('export NDEX_PWD=\'your-ndex-password\'', stderr()) | |
stop(message) | |
} else { | |
ndexcon <- ndex_connect(username=NDEX_USER, password=NDEX_PWD, host="dev2.ndexbio.org", ndexConf=ndex_config$Version_2.0) | |
} | |
tryCatch({ | |
ndex_network_set_systemProperties(ndexcon, NETWORK_ID, readOnly=FALSE) | |
}, warning = function(w) { | |
write(paste("Warning making network editable in download_upload.R:", w, sep = '\n'), stderr()) | |
NA | |
}, error = function(err) { | |
write(paste("Error making network editable in download_upload.R:", err, sep = '\n'), stderr()) | |
NA | |
}, finally = { | |
# Do something | |
}) | |
rcx <- ndex_get_network(ndexcon, NETWORK_ID) | |
networkIdCreated <- ndex_create_network(ndexcon, rcx) | |
print(networkIdCreated) | |
#networkIdUpdated <- ndex_update_network(ndexcon, rcx, NETWORK_ID) | |
#print(networkIdUpdated) |
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