Add source for Ensembl

src/pyobo/api/names.py

@@ -211,6 +211,9 @@ def get_id_name_mapping(
         rv = get_ncbigene_id_to_name_mapping()
         logger.info("[%s] done loading identifiers", prefix)
         return rv
+    if prefix == "ensembl":
+        # FIXME implement!
+        return {}
 
     version = get_version_from_kwargs(prefix, kwargs)
     path = get_cache_path(prefix, CacheArtifact.names, version=version)

src/pyobo/sources/ensembl.py

@@ -0,0 +1,38 @@
+"""Download ensembl."""
+
+from pathlib import Path
+
+import requests
+from pystow.utils import get_soup
+from tqdm import tqdm
+
+from pyobo.utils.path import ensure_path
+
+PREFIX = "ensembl"
+
+
+def get_files(*, force: bool = False) -> dict[str, Path]:
+    """Ensure all JSON files from Ensembl"""
+    version_res = requests.get("https://ftp.ensembl.org/pub/VERSION", timeout=5)
+    version_res.raise_for_status()
+    version: str = version_res.text.strip()
+    soup = get_soup("https://ftp.ensembl.org/pub/current/json/")
+    rv = {}
+    for row in tqdm(soup.find_all("tr")):
+        cells = list(row.find_all("td"))
+        if len(cells) < 2 or cells[1].text == "Parent Directory":
+            continue
+        if (anchor := cells[1].find("a")) and anchor.text:
+            name = anchor.text.strip("/")
+            url = f"https://ftp.ensembl.org/pub/current/json/{name}/{name}.json"
+            rv[name] = ensure_path(PREFIX, url=url, version=version, force=force)
+    return rv
+
+
+def main() -> None:
+    """Download it all."""
+    get_files()
+
+
+if __name__ == "__main__":
+    main()