pandora_lib_promethion/:

use std::{
    fs::{self, File, Metadata}, io::Read, path::PathBuf, str::FromStr
};

use anyhow::{anyhow, Context};
use glob::glob;
use hashbrown::HashMap;
use log::warn;
use pandora_lib_bindings::{
    progs::cramino::{Cramino, CraminoRes},
    utils::RunBin,
};
use rayon::prelude::*;
use serde::{Deserialize, Serialize};

#[derive(Debug, Clone, Deserialize, Serialize)]
pub struct Bam {
    pub id: String,
    pub time_point: String,
    pub reference_genome: String,
    pub bam_type: BamType,
    pub path: PathBuf,
    #[serde(with = "metadata_serde")]
    pub file_metadata: Metadata,
    // #[serde(skip)]
// pub file_metadata: Metadata,
    pub cramino: Option<CraminoRes>,
    pub composition: Vec<(String, f64)>,
}

#[derive(Debug, PartialEq, Clone, Deserialize, Serialize)]
pub enum BamType {
    WGS,
    Panel(String),
    ChIP(String),
}

impl Bam {
    pub fn new(path: PathBuf) -> anyhow::Result<Self> {
        let stem = path
            .clone()
            .file_stem()
            .context("Can't parse stem from {path}")?
            .to_string_lossy()
            .to_string();
        let stem: Vec<&str> = stem.split('_').collect();

        if stem.len() > 4 || stem.len() < 3 {
            return Err(anyhow!("Error in bam name: {}", path.display()));
        }

        let id = stem[0].to_string();
        let time_point = stem[1].to_string();
        let reference_genome = stem
            .last()
            .context("Can't get last from stem {stem}")?
            .to_string();

        let bam_type = if stem.len() == 4 {
            match stem[2] {
                "oncoT" => BamType::Panel("oncoT".to_string()),
                "H3K27ac" => BamType::ChIP("H3K27ac".to_string()),
                "H3K4me3" => BamType::ChIP("H3K4me3".to_string()),
                _ => return Err(anyhow!("Error in bam name: {}", path.display())),
            }
        } else {
            BamType::WGS
        };

        let tp_dir = path
            .parent()
            .context("Can't parse parent from: {bam_path}")?;
        let cramino_path = format!(
            "{}/{id}_{time_point}_hs1_cramino.txt",
            tp_dir.to_string_lossy()
        );
        let file_metadata = fs::metadata(&path)?;

        let cramino = if bam_type == BamType::WGS {
            if !PathBuf::from_str(&cramino_path)?.exists() {
                return Err(anyhow!("Cramino file missing {cramino_path}"));
            }
            let mut cramino = Cramino::default().with_result_path(&cramino_path);
            cramino
                .parse_results()
                .context(format!("Error while parsing cramino for {cramino_path}"))?;

            if let Some(cramino) = cramino.results {
                Some(cramino)
            } else {
                return Err(anyhow!("Cramino results parsing failed"));
            }
        } else {
            None
        };

        let composition =
            pandora_lib_pileup::bam_compo(path.to_string_lossy().as_ref(), 20000).context(
                format!("Error while reading BAM composition for {}", path.display()),
            )?;

        Ok(Self {
            path,
            // file_metadata,
            cramino,
            id: id.to_string(),
            time_point: time_point.to_string(),
            bam_type,
            reference_genome,
            composition,
        })
    }

    pub fn load_json(path: &str) -> anyhow::Result<Self> {
        let f = File::open(path)?;
        let s: Self = serde_json::from_reader(f)?;
        Ok(s)
    }

    pub fn save_json(path: &str) -> anyhow::Result<()> {

    }
}

#[derive(Debug)]
pub struct BamCollection {
    pub bams: Vec<Bam>,
}

impl BamCollection {
    pub fn new(result_dir: &str) -> Self {
        load_bam_collection(result_dir)
    }

    pub fn by_acquisition_id(&self) -> HashMap<String, Vec<&Bam>> {
        let mut acq: HashMap<String, Vec<&Bam>> = HashMap::new();
        for bam in self.bams.iter() {
            for (acq_id, _) in bam.composition.iter() {
                if let Some(entry) = acq.get_mut(acq_id) {
                    entry.push(bam);
                } else {
                    acq.insert(acq_id.to_string(), vec![bam]);
                }
            }
        }
        acq
    }

    pub fn get(&self, id: &str, time_point: &str) -> Vec<&Bam> {
        self.bams
            .iter()
            .filter(|b| b.id == id && b.time_point == time_point)
            .collect()
    }

    pub fn by_id_completed(&self, min_diag_cov: f32, min_mrd_cov: f32) -> Vec<Bam> {
        self.bams
            .iter()
            .filter(|b| matches!(b.bam_type, BamType::WGS))
            .filter(|b| match &b.cramino {
                Some(cramino) => match b.time_point.as_str() {
                    "diag" => cramino.mean_length >= min_diag_cov as f64,
                    "mrd" => cramino.mean_length >= min_mrd_cov as f64,
                    _ => false
                },
                _ => false,
            })
            .cloned()
            .collect()
    }
}

pub fn load_bam_collection(result_dir: &str) -> BamCollection {
    let pattern = format!("{}/*/*/*.bam", result_dir);
    let bams = glob(&pattern)
        .expect("Failed to read glob pattern")
        .par_bridge()
        .filter_map(|entry| {
            match entry {
                Ok(path) => match Bam::new(path) {
                    Ok(bam) => return Some(bam),
                    Err(e) => warn!("{e}"),
                },
                Err(e) => warn!("Error: {:?}", e),
            }
            None
        })
        .collect();

    BamCollection { bams }
}

mod metadata_serde {
    use super::*;
    use serde::{Serializer, Deserializer};

    #[derive(Serialize, Deserialize)]
    struct SerializableMetadata {
        len: u64,
        modified: u64,
        created: u64,
    }

    pub fn serialize<S>(metadata: &Metadata, serializer: S) -> Result<S::Ok, S::Error>
    where
        S: Serializer,
    {
        let serializable = SerializableMetadata {
            len: metadata.len(),
            modified: metadata.modified()
                .unwrap_or(UNIX_EPOCH)
                .duration_since(UNIX_EPOCH)
                .unwrap_or_default()
                .as_secs(),
            created: metadata.created()
                .unwrap_or(UNIX_EPOCH)
                .duration_since(UNIX_EPOCH)
                .unwrap_or_default()
                .as_secs(),
        };
        serializable.serialize(serializer)
    }

    pub fn deserialize<'de, D>(deserializer: D) -> Result<Metadata, D::Error>
    where
        D: Deserializer<'de>,
    {
        let serializable = SerializableMetadata::deserialize(deserializer)?;
        let file = tempfile::tempfile().map_err(serde::de::Error::custom)?;
        let metadata = file.metadata().map_err(serde::de::Error::custom)?;
        Ok(metadata)
    }
}