Nothing
## Check if we are running on travis
on_travis <- function() {
if (identical(Sys.getenv("TRAVIS"), "true")) {
return(TRUE)
# nocov start
} else {
return(FALSE)
}
# nocov end
}
## Look up env vars and log in to Synapse
syn_travis_login <- function(syn) {
## Credentials are encrypted on travis
user <- Sys.getenv("SYNAPSE_USER")
pass <- Sys.getenv("SYNAPSE_PASSWORD")
syn$login(email = user, password = pass)
}
attempt_instantiate <- function() {
if (reticulate::py_module_available("synapseclient")) {
return(synapse$Synapse())
} else {
return(NULL)
}
}
## Attempt to log in using encrypted travis variables if on travis within Sage
## org, or with regular synLogin() if not on travis. If on travis but not within
## Sage, do nothing.
attempt_login <- function(syn, ...) {
if (on_travis() & !is.null(syn)) {
try(syn_travis_login(syn), silent = TRUE)
} else if (reticulate::py_module_available("synapseclient") & !is.null(syn)) {
syn$login(...)
} else {
return(NULL)
}
}
## Check if we're logged in
logged_in <- function(syn) {
if (is.null(syn) || is.null(syn$username)) {
return(FALSE)
} else {
return(TRUE)
}
}
## Save uploaded files to Synapse
save_to_synapse <- function(input_file,
parent,
annotations = NULL,
synapseclient,
syn) {
if (!is_name_valid(input_file$name)) {
stop("Please check that file names only contain: letters, numbers, spaces, underscores, hyphens, periods, plus signs, and parentheses.") # nolint
}
file_to_upload <- synapseclient$File(
input_file$datapath,
parent = parent,
name = input_file$name,
annotations = annotations
)
syn$store(file_to_upload)
}
"%||%" <- function(a, b) {
if (!is.null(a)) a else b
}
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