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get_request <-function(url){
qr = URLencode(url)
response <- GET( qr )
if(status_code(response) != 200) {
stop(
paste(
"Error running query. Received HTTP error code",
status_code(response),
"from server. Please try again later. If you continue to experience
problems please contact us
at https://www.ebi.ac.uk/about/contact/support/arrayexpress"
)
)
}
json_parsed <- fromJSON(txt = qr)
return(json_parsed)
}
queryAE = function(keywords = NULL, species = NULL){
if(is.null(keywords) && is.null(species))
stop("No keywords or species specified")
baseURL <- "https://www.ebi.ac.uk/biostudies/api/v1/arrayexpress/search";
page_size <- 100
page=1
query <- paste(baseURL,"?query=",keywords,"&organism=",species,"&pageSize=",
page_size,sep="")
json_data <- get_request(paste(query,"&page=",page,sep=""))
df_hits <- json_data$hits
while (length(json_data$hits) > 0) {
page <- page + 1
json_data <- get_request(paste(query,"&page=",page,sep=""))
if (length(json_data$hits) > 0) {
df_hits <- rbind(df_hits, json_data$hits)
}
}
return(df_hits)
}
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