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Merged
Chris7 merged 1 commit into from
Apr 8, 2025
Merged

Support gzipped genbanks #170

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22 changes: 17 additions & 5 deletions src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ use gen::exports::fasta::export_fasta;
use gen::exports::genbank::export_genbank;
use gen::exports::gfa::export_gfa;
use gen::fasta::FastaError;
use gen::genbank::GenBankError;
use gen::get_connection;
use gen::graph_operators::{derive_chunks, get_path, make_stitch};
use gen::imports::fasta::import_fasta;
Expand Down Expand Up @@ -608,11 +609,16 @@ fn main() {
}
}
} else if let Some(gb) = gb {
let f = File::open(gb).unwrap();
let _ = import_genbank(
let mut reader: Box<dyn std::io::Read> = if gb.ends_with(".gz") {
let file = File::open(gb.clone()).unwrap();
Box::new(flate2::read::GzDecoder::new(file))
} else {
Box::new(File::open(gb.clone()).unwrap())
};
match import_genbank(
&conn,
&operation_conn,
&f,
&mut reader,
name.deref(),
sample.as_deref(),
OperationInfo {
Expand All @@ -622,8 +628,14 @@ fn main() {
}],
description: "GenBank Import".to_string(),
},
);
println!("Genbank imported.");
) {
Ok(_) => println!("GenBank Imported."),
Err(err) => {
conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
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@dkhofer dkhofer Apr 8, 2025

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Nice. I have a to-do to make sure all commands roll back on errors, eventually

operation_conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
panic!("Import failed: {err:?}");
}
}
} else if region_name.is_some() && parts.is_some() && library.is_some() {
import_library(
&conn,
Expand Down