Read the leaderboard information for the Prostate Cancer DREAM Challenge into a data.frame

get_leaderboard.R

library(plyr)
library(synapseClient)
synapseLogin('chris.bare')


## Q1a = 3317421, Q1b = 3317433, Q2 = 3317446
## https://www.synapse.org/#!Synapse:syn2762531/wiki/72477
## metrics in the query may need to change for different questions
eid = '3317421'

total = .Machine$integer.max
limit = 50
offset = 0

blocks = list()
i = 0

## read blocks of rows from Synapse
while (offset < total) {
    fields = paste('objectId', 'status', 'createdOn', 'modifiedOn', 'team', 'name', 'cIndex', 'auc12', 'auc18', 'auc24', 'iAUC', sep=",+")
    uri = sprintf("/evaluation/submission/query?query=select+%s+from+evaluation_%s+where+status==\"SCORED\"+limit+%d+offset+%d", fields, eid, limit, offset)
    results <- synRestGET(uri)

    ## massage data into data.frames
    m <- do.call(rbind, lapply(results$rows, function(row) { row$values }))
    colnames(m) <- results$headers
    df <- as.data.frame(m)
    i <- i + 1
    blocks[[i]] <- df

    total <- results$totalNumberOfResults
    offset <- offset + limit
}

## combine rows to a data.frame using plyr's rbind.fill
df <- rbind.fill(blocks)