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📝 CodeRabbit Chat: Fix Spectronaut CSV column selection for Datasets API #20

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📝 CodeRabbit Chat: Fix Spectronaut CSV column selection for Datasets API #20

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15 changes: 11 additions & 4 deletions R/clean_spectronaut.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,15 @@ reduceBigSpectronaut <- function(input_file, output_path,
delim <- ";"
}

# Columns cleanSpectronautChunk actually consumes; Arrow's
# convert_options$include_columns drops everything else at parse time so
# we never materialize the ~35 unused columns Spectronaut exports.
# Columns cleanSpectronautChunk actually consumes; only these are
# projected out of the dataset so we never materialize the ~35 unused
# columns Spectronaut exports. Note: CsvConvertOptions$include_columns
# only applies to the one-shot read_csv_arrow() reader -- it is silently
# ignored by the Datasets API (open_dataset() + Scanner) used below, so
# column pruning has to happen via Scanner$create(projection = ...)
# instead. present_cols intersects with the file's actual schema so
# older/variant Spectronaut exports missing an optional column don't
# make the scan fail on an unknown column name.
needed_cols <- c("R.FileName", "R.Condition", "R.Replicate",
"PG.ProteinAccessions", "EG.ModifiedSequence",
"FG.LabeledSequence", "FG.Charge",
Expand Down Expand Up @@ -55,7 +61,8 @@ reduceBigSpectronaut <- function(input_file, output_path,
read_options = read_opts
)

reader <- arrow::Scanner$create(ds)$ToRecordBatchReader()
present_cols <- intersect(needed_cols, ds$schema$names)
reader <- arrow::Scanner$create(ds, projection = present_cols)$ToRecordBatchReader()

t_start <- Sys.time()
pos <- 1L
Expand Down