ctddump 0.29.0

Convert oceanographic CTD (Conductivity, Temperature, Depth) data from NetCDF to Parquet or YAML
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use std::fs;
use ctddump::handle_dispatch;
use polars::prelude::*;

// ── helpers ──────────────────────────────────────────────────────────────────

/// Copy `src` files into a fresh temp dir and return (temp_dir, dir_path).
fn setup_src(files: &[&str]) -> (tempfile::TempDir, std::path::PathBuf) {
    let dir = tempfile::tempdir().unwrap();
    for f in files {
        fs::copy(f, dir.path().join(std::path::Path::new(f).file_name().unwrap())).unwrap();
    }
    let path = dir.path().to_path_buf();
    (dir, path)
}

/// Batch-convert NC files to Parquet, return the output dir.
fn make_parquet_dir(nc_files: &[&str], subcommand: &str) -> tempfile::TempDir {
    let out_dir = tempfile::tempdir().unwrap();
    let (_src_guard, src_dir) = setup_src(nc_files);
    let args: Vec<String> = vec![
        "batch".to_string(), "convert".to_string(), subcommand.to_string(),
        "--output".to_string(), out_dir.path().to_str().unwrap().to_string(),
        src_dir.to_str().unwrap().to_string(),
    ];
    handle_dispatch(&args).unwrap();
    out_dir
}

/// Batch-extract header YAML files, return the output dir.
fn make_yaml_dir(nc_files: &[&str], subcommand: &str) -> tempfile::TempDir {
    let out_dir = tempfile::tempdir().unwrap();
    let (_src_guard, src_dir) = setup_src(nc_files);
    let args: Vec<String> = vec![
        "batch".to_string(), "header".to_string(), subcommand.to_string(),
        "--output".to_string(), out_dir.path().to_str().unwrap().to_string(),
        src_dir.to_str().unwrap().to_string(),
    ];
    handle_dispatch(&args).unwrap();
    out_dir
}

fn read_parquet(path: &std::path::Path) -> DataFrame {
    let f = std::fs::File::open(path).unwrap();
    ParquetReader::new(f).finish().unwrap()
}

// ── concat convert: basic merge ───────────────────────────────────────────────

#[test]
fn test_concat_convert_merges_files_into_one() {
    let parquet_dir = make_parquet_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc", "./tests/test_data/AR_PR_CT_58KN.nc"],
        "nrt_ar",
    );
    let output = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();

    let args = vec![
        "concat".to_string(), "convert".to_string(),
        parquet_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());
    assert!(output.path().exists());

    let combined = read_parquet(output.path());
    let itp71 = read_parquet(&parquet_dir.path().join("AR_PR_CT_ITP-71.parquet"));
    let kn58  = read_parquet(&parquet_dir.path().join("AR_PR_CT_58KN.parquet"));
    assert_eq!(combined.height(), itp71.height() + kn58.height());
}

// ── concat convert: profile_no renumbering ────────────────────────────────────

#[test]
fn test_concat_convert_renumber_profile_no_starts_at_one() {
    let parquet_dir = make_parquet_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc", "./tests/test_data/AR_PR_CT_58KN.nc"],
        "nrt_ar",
    );
    let output = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();

    let args = vec![
        "concat".to_string(), "convert".to_string(),
        parquet_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());

    let df = read_parquet(output.path());
    let min = df.column("profile_no").unwrap().min::<u32>().unwrap().unwrap();
    assert_eq!(min, 1, "profile_no should start at 1");
}

#[test]
fn test_concat_convert_renumber_observation_no_starts_at_one() {
    let parquet_dir = make_parquet_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc"],
        "nrt_ar",
    );
    let output = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();

    let args = vec![
        "concat".to_string(), "convert".to_string(),
        parquet_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());

    let df = read_parquet(output.path());
    let min = df.column("observation_no").unwrap().min::<u32>().unwrap().unwrap();
    assert_eq!(min, 1, "observation_no should start at 1");
}

// ── concat convert: --no-pres-sort ────────────────────────────────────────────

/// Write a single-profile Parquet file whose observations are in *descending* pres
/// order (i.e. not sorted by pressure), then merge it with and without
/// `--no-pres-sort` and check the resulting per-observation `pres` order.
#[test]
fn test_concat_convert_no_pres_sort_preserves_source_order() {
    let dir = tempfile::tempdir().unwrap();

    // One platform, one profile (shared timestamp/lon/lat); pres runs 30 -> 10.
    let mut df = df!(
        "platform_code"     => ["P", "P", "P"],
        "profile_timestamp" => [1000i64, 1000, 1000],
        "longitude"         => [10.0f64, 10.0, 10.0],
        "latitude"          => [60.0f64, 60.0, 60.0],
        "pres"              => [30.0f32, 20.0, 10.0],
        "profile_no"        => [0u32, 0, 0],
        "observation_no"    => [0u32, 0, 0],
    )
    .unwrap();
    let src = dir.path().join("in.parquet");
    ParquetWriter::new(std::fs::File::create(&src).unwrap())
        .finish(&mut df)
        .unwrap();

    let run = |extra: &[&str]| -> Vec<f32> {
        let out = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();
        let mut args = vec!["concat".to_string(), "convert".to_string()];
        args.extend(extra.iter().map(|s| s.to_string()));
        args.push(dir.path().to_str().unwrap().to_string());
        args.push(out.path().to_str().unwrap().to_string());
        assert!(handle_dispatch(&args).is_ok());
        let df = read_parquet(out.path());
        df.column("pres").unwrap().f32().unwrap().into_no_null_iter().collect()
    };

    // Default: sorted ascending by pres.
    assert_eq!(run(&[]), vec![10.0, 20.0, 30.0]);
    // --no-pres-sort: keep the original (descending) source order.
    assert_eq!(run(&["--no-pres-sort"]), vec![30.0, 20.0, 10.0]);
}

// ── concat convert: missing-pres dropping (default on) ────────────────────────

/// A single profile with NaN `pres` interleaved among valid rows. By default the
/// NaN rows are removed before numbering, leaving `pres` fully populated and
/// `observation_no` contiguous (1..N); `--keep-na-pres` retains all rows.
#[test]
fn test_concat_convert_drops_na_pres_by_default() {
    let dir = tempfile::tempdir().unwrap();

    let mut df = df!(
        "platform_code"     => ["P", "P", "P", "P", "P"],
        "profile_timestamp" => [1000i64, 1000, 1000, 1000, 1000],
        "longitude"         => [10.0f64, 10.0, 10.0, 10.0, 10.0],
        "latitude"          => [60.0f64, 60.0, 60.0, 60.0, 60.0],
        "pres"              => [10.0f32, f32::NAN, 20.0, f32::NAN, 30.0],
        "profile_no"        => [0u32, 0, 0, 0, 0],
        "observation_no"    => [0u32, 0, 0, 0, 0],
    )
    .unwrap();
    let src = dir.path().join("in.parquet");
    ParquetWriter::new(std::fs::File::create(&src).unwrap())
        .finish(&mut df)
        .unwrap();

    let run = |extra: &[&str]| -> DataFrame {
        let out = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();
        let mut args = vec!["concat".to_string(), "convert".to_string()];
        args.extend(extra.iter().map(|s| s.to_string()));
        args.push(dir.path().to_str().unwrap().to_string());
        args.push(out.path().to_str().unwrap().to_string());
        assert!(handle_dispatch(&args).is_ok());
        read_parquet(out.path())
    };

    // Default: the two NaN-pres rows are dropped.
    let dropped = run(&[]);
    assert_eq!(dropped.height(), 3, "NaN-pres rows should be removed by default");
    let pres: Vec<f32> = dropped.column("pres").unwrap().f32().unwrap().into_no_null_iter().collect();
    assert_eq!(pres, vec![10.0, 20.0, 30.0]);
    let obs: Vec<u32> = dropped.column("observation_no").unwrap().u32().unwrap().into_no_null_iter().collect();
    assert_eq!(obs, vec![1, 2, 3], "observation_no must be contiguous after dropping");

    // --keep-na-pres: all 5 rows retained.
    assert_eq!(run(&["--keep-na-pres"]).height(), 5);
}

// ── concat convert: --no-renumber ─────────────────────────────────────────────

#[test]
fn test_concat_convert_no_renumber_preserves_row_count() {
    let parquet_dir = make_parquet_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc", "./tests/test_data/AR_PR_CT_58KN.nc"],
        "nrt_ar",
    );
    let output = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();

    let args = vec![
        "concat".to_string(), "convert".to_string(),
        "--no-renumber".to_string(),
        parquet_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());

    let combined = read_parquet(output.path());
    let itp71 = read_parquet(&parquet_dir.path().join("AR_PR_CT_ITP-71.parquet"));
    let kn58  = read_parquet(&parquet_dir.path().join("AR_PR_CT_58KN.parquet"));
    assert_eq!(combined.height(), itp71.height() + kn58.height());
}

// ── concat convert: --pattern ─────────────────────────────────────────────────

#[test]
fn test_concat_convert_pattern_selects_subset() {
    let parquet_dir = make_parquet_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc", "./tests/test_data/AR_PR_CT_58KN.nc"],
        "nrt_ar",
    );
    let output = tempfile::NamedTempFile::with_suffix(".parquet").unwrap();

    let args = vec![
        "concat".to_string(), "convert".to_string(),
        "--pattern".to_string(), "AR_PR_CT_ITP-71.parquet".to_string(),
        parquet_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());

    let combined = read_parquet(output.path());
    let itp71 = read_parquet(&parquet_dir.path().join("AR_PR_CT_ITP-71.parquet"));
    assert_eq!(combined.height(), itp71.height());
}

// ── concat convert: error cases ───────────────────────────────────────────────

/// An empty input directory is not an error: concat succeeds and writes no output.
#[test]
fn test_concat_convert_empty_no_output() {
    let src_dir = tempfile::tempdir().unwrap();
    let out_dir = tempfile::tempdir().unwrap();
    let output  = out_dir.path().join("merged.parquet");

    let args = vec![
        "concat".to_string(), "convert".to_string(),
        src_dir.path().to_str().unwrap().to_string(),
        output.to_str().unwrap().to_string(),
    ];
    let result = handle_dispatch(&args);
    assert!(result.is_ok(), "empty input should succeed, got: {result:?}");
    assert!(!output.exists(), "no output file should be created");
}

// ── concat header: basic merge ────────────────────────────────────────────────

#[test]
fn test_concat_header_merges_yaml_files() {
    let yaml_dir = make_yaml_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc", "./tests/test_data/AR_PR_CT_58KN.nc"],
        "nrt",
    );
    let output = tempfile::NamedTempFile::with_suffix(".yaml").unwrap();

    let args = vec![
        "concat".to_string(), "header".to_string(),
        yaml_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());
    assert!(output.path().exists());

    // Output must contain both file stem keys
    let content = fs::read_to_string(output.path()).unwrap();
    assert!(content.contains("AR_PR_CT_ITP-71"), "missing ITP-71 key");
    assert!(content.contains("AR_PR_CT_58KN"),   "missing 58KN key");
}

#[test]
fn test_concat_header_pattern_selects_subset() {
    let yaml_dir = make_yaml_dir(
        &["./tests/test_data/AR_PR_CT_ITP-71.nc", "./tests/test_data/AR_PR_CT_58KN.nc"],
        "nrt",
    );
    let output = tempfile::NamedTempFile::with_suffix(".yaml").unwrap();

    let args = vec![
        "concat".to_string(), "header".to_string(),
        "--pattern".to_string(), "AR_PR_CT_ITP-71.yaml".to_string(),
        yaml_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    assert!(handle_dispatch(&args).is_ok());

    let content = fs::read_to_string(output.path()).unwrap();
    assert!( content.contains("AR_PR_CT_ITP-71"), "missing ITP-71 key");
    assert!(!content.contains("AR_PR_CT_58KN"),   "58KN should not be present");
}

/// An empty input directory is not an error: concat header succeeds and writes no output.
#[test]
fn test_concat_header_empty_no_output() {
    let src_dir = tempfile::tempdir().unwrap();
    let out_dir = tempfile::tempdir().unwrap();
    let output  = out_dir.path().join("merged.yaml");

    let args = vec![
        "concat".to_string(), "header".to_string(),
        src_dir.path().to_str().unwrap().to_string(),
        output.to_str().unwrap().to_string(),
    ];
    let result = handle_dispatch(&args);
    assert!(result.is_ok(), "empty input should succeed, got: {result:?}");
    assert!(!output.exists(), "no output file should be created");
}

#[test]
fn test_concat_header_duplicate_key_error() {
    // Two copies of the same YAML file → same top-level key → duplicate error
    let yaml_dir = make_yaml_dir(&["./tests/test_data/AR_PR_CT_ITP-71.nc"], "nrt");
    // Write a duplicate of the produced YAML under a different filename but same key inside
    let src_yaml = yaml_dir.path().join("AR_PR_CT_ITP-71.yaml");
    fs::copy(&src_yaml, yaml_dir.path().join("AR_PR_CT_ITP-71_copy.yaml")).unwrap();

    let output = tempfile::NamedTempFile::with_suffix(".yaml").unwrap();
    let args = vec![
        "concat".to_string(), "header".to_string(),
        yaml_dir.path().to_str().unwrap().to_string(),
        output.path().to_str().unwrap().to_string(),
    ];
    let result = handle_dispatch(&args);
    assert!(result.is_err());
    assert!(result.unwrap_err().to_string().contains("Duplicate keys"));
}