Merge pull request #297 from scverse/refactor/ensmbl-to-symbol-download

Refactor ensmbl_to_symbol to reuse _download

Author: PauBadiaM

CHANGELOG.md

@@ -13,6 +13,9 @@ and this project adheres to [Semantic Versioning][].
 ### Added
 - `pl.volcano` now accepts a gene name (`str`) or list of gene names (`list[str]`) for the `top` parameter to annotate specific features on volcano plots
 
+### Changes
+- Refactored `ds.ensmbl_to_symbol` to reuse `_download` and fixed mirror fallback to actually switch between Ensembl mirrors
+
 ## 2.1.4
 
 ### Changes

src/decoupler/ds/_utils.py

@@ -1,7 +1,8 @@
 import io
 
 import pandas as pd
-import requests
+
+from decoupler._download import _download
 
 
 def ensmbl_to_symbol(
@@ -29,7 +30,7 @@ def ensmbl_to_symbol(
         dc.ds.ensmbl_to_symbol(genes=["ENSG00000196092", "ENSG00000115415"], organism="hsapiens_gene_ensembl")
     """
     url = (
-        'http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>'
+        'http://{mirror}.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?>'
         '<!DOCTYPE Query><Query  virtualSchemaName = "default" formatter = "TSV" header = "0" un'
         'iqueRows = "0" count = "" ><Dataset name = "{organism}" '
         'interface = "default" ><Attribute name = "ensembl_gene_id" /><Attribute name ='
@@ -47,16 +48,24 @@ def ensmbl_to_symbol(
     assert isinstance(genes, list), "genes must be list"
     assert isinstance(organism, str), "organism must be str"
     # Try different mirrors
-    response = requests.get(url.format(miror="www", organism=organism))
-    if any(msg in response.text for msg in ["Service unavailable", "Gateway Time-out"]):
-        response = requests.get(url.format(miror="useast", organism=organism))
-    if any(msg in response.text for msg in ["Service unavailable", "Gateway Time-out"]):
-        response = requests.get(url.format(miror="asia", organism=organism))
-    if not any(msg in response.text for msg in ["Service unavailable", "Gateway Time-out"]):
-        eids = pd.read_csv(io.StringIO(response.text), sep="\t", header=None, index_col=0)[1].to_dict()
-    elif organism in ["hsapiens_gene_ensembl", "mmusculus_gene_ensembl"]:
+    error_msgs = ["Service unavailable", "Gateway Time-out"]
+    for mirror in ["www", "useast", "uswest", "asia"]:
+        try:
+            data = _download(url.format(mirror=mirror, organism=organism))
+            text = data.read().decode()
+            if any(msg in text for msg in error_msgs) or not text.strip():
+                continue
+            df = pd.read_csv(io.StringIO(text), sep="\t", header=None, index_col=0)
+            if df.empty or 1 not in df.columns:
+                continue
+            eids = df[1].to_dict()
+            return [eids[g] if g in eids else None for g in genes]
+        except Exception:
+            continue
+    # Zenodo fallback for human and mouse
+    if organism in ["hsapiens_gene_ensembl", "mmusculus_gene_ensembl"]:
         url = f"https://zenodo.org/records/15551885/files/{organism}.csv.gz?download=1"
-        eids = pd.read_csv(url, index_col=0, compression="gzip")["symbol"].to_dict()
-    else:
-        assert AssertionError(), "ensembl servers are down, try again later"
-    return [eids[g] if g in eids else None for g in genes]
+        data = _download(url)
+        eids = pd.read_csv(data, index_col=0, compression="gzip")["symbol"].to_dict()
+        return [eids[g] if g in eids else None for g in genes]
+    raise ValueError("ensembl servers are down, try again later")