feat: use wags-tails for data management

pyproject.toml

@@ -24,7 +24,7 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
 ]
-dependencies = []
+dependencies = ["wags-tails"]
 
 [project.optional-dependencies]
 test = [

rust/src/lib.rs

@@ -1,46 +1,12 @@
 //! Provide Rust-based chainfile wrapping classes.
 use chain::core::{Coordinate, Interval, Strand};
 use chainfile as chain;
-use directories::BaseDirs;
-use pyo3::exceptions::PyValueError;
+use pyo3::exceptions::{PyValueError, PyFileNotFoundError};
 use pyo3::prelude::*;
-use std::env;
-use std::fs;
 use std::fs::File;
 use std::io::BufReader;
 use std::path::Path;
 
-fn get_chainfile_dir() -> String {
-    let env_var_name = "CHAINLIFTER_DATA_DIR";
-    if let Ok(value) = env::var(env_var_name) {
-        return value;
-    } else if let Some(base_dirs) = BaseDirs::new() {
-        let data_dir = base_dirs.home_dir();
-        let base_chainfile_dir = format!("{}/.local/share/chainlifter", data_dir.display());
-        return base_chainfile_dir;
-    } else {
-        panic!("Unable to get ChainLifter data directory.")
-    }
-}
-
-/// Acquire chainfile.
-/// TODO: fetch from remote if not available locally, probably via config
-/// TODO: throw exceptions if unable to acquire
-/// TODO: specify base dir
-fn get_chainfile(from_db: &str, to_db: &str) -> String {
-    let base_chainfile_dir = get_chainfile_dir();
-    fs::create_dir_all(base_chainfile_dir.clone()).unwrap();
-    let path = format!(
-        "{}/hg{}ToHg{}.over.chain",
-        base_chainfile_dir, from_db, to_db
-    );
-    if Path::new(&path).exists() {
-        path
-    } else {
-        "this isn't going to work".to_string()
-    }
-}
-
 /// Define core ChainLifter class to be used by Python interface.
 /// Effectively just a wrapper on top of the chainfile crate's Machine struct.
 #[pyclass]
@@ -51,14 +17,16 @@ pub struct ChainLifter {
 #[pymethods]
 impl ChainLifter {
     #[new]
-    pub fn new(from_db: &str, to_db: &str) -> ChainLifter {
-        let chainfile_name: String = get_chainfile(from_db, to_db);
-        let data = BufReader::new(File::open(&chainfile_name).unwrap());
+    pub fn new(chainfile_path: &str) -> PyResult<ChainLifter> {
+        if !Path::new(&chainfile_path).exists() {
+            return Err(PyFileNotFoundError::new_err("Chainfile doesn't exist"));
+        }
+        let data = BufReader::new(File::open(&chainfile_path).unwrap());
         let reader = chain::Reader::new(data);
         let machine = chain::liftover::machine::Builder::default()
             .try_build_from(reader)
             .unwrap();
-        ChainLifter { machine }
+        Ok(ChainLifter { machine })
     }
 
     /// Perform liftover

src/chainlifter/lifter.py

@@ -1,5 +1,12 @@
 """Perform chainfile-driven liftover."""
+from pathlib import Path
 from enum import Enum
+from typing import Callable
+
+import requests
+from wags_tails import CustomData, DataSource
+from wags_tails.utils.downloads import handle_gzip, download_http
+from wags_tails.utils.storage import get_data_dir
 
 import chainlifter._core as _core
 
@@ -22,7 +29,38 @@ def __init__(self, from_db: str, to_db: str) -> None:
         :param from_db: database name, e.g. ``"19"``
         :param to_db: database name, e.g. ``"38"``
         """
-        self._chainlifter = _core.ChainLifter(from_db, to_db)
+        data_handler = CustomData(
+            f"chainfile_{from_db}_to_{to_db}",
+            "chain",
+            lambda: "",
+            self._download_function_builder(from_db, to_db),
+            data_dir=get_data_dir() / "ucsc-chainfile",
+        )
+        file, _ = data_handler.get_latest()
+        self._chainlifter = _core.ChainLifter(str(file.absolute()))
+
+    @staticmethod
+    def _download_function_builder(from_db: str, to_db: str) -> Callable:
+        """Build downloader function for chainfile corresponding to source/destination
+        params.
+
+        Wags-Tails' custom data handler takes a downloader callback function. We
+        construct it here, curried with from/to values in the download URL.
+
+        :param from_db: genome lifting from
+        :param to_db: genome lifting to
+        :return: Function that downloads appropriate chainfile from UCSC
+        """
+        def _download_data(version: str, file: Path) -> None:
+            """Download and gunzip chainfile from UCSC.
+
+            :param version: not used
+            :param file: path to save file to
+            """
+            url = f"https://hgdownload.soe.ucsc.edu/goldenPath/{from_db}/liftOver/{from_db}To{to_db.title()}.over.chain.gz"
+            download_http(url, file, handler=handle_gzip)
+
+        return _download_data
 
     def convert_coordinate(
         self, chrom: str, pos: int, strand: Strand = Strand.POSITIVE
@@ -35,7 +73,7 @@ def convert_coordinate(
 
            from chainlifter.lifter import ChainLifter, Strand
 
-           lifter = ChainLifter("19", "38")
+           lifter = ChainLifter("hg19", "hg38")
            lifter.convert_coordinate("chr7", 140453136, Strand.POSITIVE)
            # returns [['chr7', '140753336', '+']]