gen 0.1.31

A sequence graph and version control system.
Documentation 
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use std::path::PathBuf;

use anyhow::Result;
use clap::Args;
use gen_models::{errors::OperationError, sample::Sample};

use crate::{
    commands::{cli_context::CliContext, get_default_collection},
    imports::gfa::{GFAImportError, import_gfa},
};

/// Import a GFA file
#[derive(Debug, Args, Clone)]
pub struct Command {
    /// GFA file path
    #[clap(index = 1)]
    pub path: String,
    /// The name of the collection to store the entry under
    #[arg(short, long)]
    name: Option<String>,
    /// A sample name to associate the GFA file with
    #[arg(short, long, default_value_t = Sample::DEFAULT_NAME.to_string())]
    sample: String,
}

pub fn execute(cli_context: &CliContext, cmd: Command) -> Result<()> {
    println!("GFA import called");

    let context = cli_context.context;
    let operation_conn = context.operations().conn();
    let conn = context.graph().conn();

    conn.execute("BEGIN TRANSACTION", []).unwrap();
    operation_conn.execute("BEGIN TRANSACTION", []).unwrap();

    let name = &cmd
        .name
        .clone()
        .unwrap_or_else(|| get_default_collection(operation_conn));
    match import_gfa(
        context,
        &PathBuf::from(cmd.path.clone()),
        name,
        cmd.sample.as_str(),
    ) {
        Ok(_) => {
            println!("GFA imported.");
            conn.execute("END TRANSACTION;", []).unwrap();
            operation_conn.execute("END TRANSACTION;", []).unwrap();
            Ok(())
        }
        Err(GFAImportError::OperationError(OperationError::NoChanges)) => {
            conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
            operation_conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
            println!("GFA already exists.");
            Ok(())
        }
        Err(e) => {
            conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
            operation_conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
            println!("Import failed.");
            Err(e.into())
        }
    }
}