gen 0.1.31

A sequence graph and version control system.
Documentation 
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use anyhow::Result;
use clap::Args;
use gen_models::{errors::OperationError, sample::Sample};

use crate::{
    commands::{cli_context::CliContext, get_default_collection},
    graphs::combinatorial_library::parse_library,
    imports::library::{LibraryImportError, import_library},
};

/// Import Library files
#[derive(Debug, Args, Clone)]
pub struct Command {
    /// The name of the library
    #[clap(index = 1)]
    library_name: String,
    /// The path to the combinatorial library parts fasta file
    #[clap(index = 2)]
    parts: Option<String>,
    /// The path to the combinatorial library csv file
    #[clap(index = 3)]
    library: Option<String>,
    /// The name of the collection to store the entry under
    #[arg(short, long)]
    name: Option<String>,
    /// A sample name to associate the library with
    #[arg(short, long, default_value_t = Sample::DEFAULT_NAME.to_string())]
    sample: String,
}

pub fn execute(cli_context: &CliContext, cmd: Command) -> Result<()> {
    println!("Library 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));
    let parts_list = parse_library(&cmd.parts.clone().unwrap(), &cmd.library.clone().unwrap())?;

    let parts_path = cmd.parts.unwrap();
    let library_path = cmd.library.unwrap();

    match import_library(
        context,
        name,
        cmd.sample.as_str(),
        &cmd.library_name,
        parts_list,
        Some(&parts_path),
        Some(&library_path),
    ) {
        Ok(_) => {
            println!("Imported library file {library_path} and parts file {parts_path}");
            conn.execute("END TRANSACTION;", []).unwrap();
            operation_conn.execute("END TRANSACTION;", []).unwrap();
            Ok(())
        }
        Err(LibraryImportError::OperationError(OperationError::NoChanges)) => {
            conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
            operation_conn.execute("ROLLBACK TRANSACTION;", []).unwrap();
            println!("Library already exists.");
            Ok(())
        }
        Err(e) => {
            println!("Library import failed: {}", e);
            Err(e.into())
        }
    }
}