From bc2ba33e3718166c8d62143ac570dcdf0f54dcde Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 26 Jul 2022 23:59:11 +0200 Subject: [PATCH] Update wikipathways download Closes #133 --- src/pyobo/sources/wikipathways.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/pyobo/sources/wikipathways.py b/src/pyobo/sources/wikipathways.py index 93ee4ab8..217266c8 100644 --- a/src/pyobo/sources/wikipathways.py +++ b/src/pyobo/sources/wikipathways.py @@ -3,6 +3,7 @@ """Converter for WikiPathways.""" import logging +import urllib.error from typing import Iterable from .gmt_utils import parse_wikipathways_gmt @@ -37,6 +38,7 @@ ("Rattus_norvegicus", "10116"), ("Saccharomyces_cerevisiae", "4932"), ("Sus_scrofa", "9823"), + ("Solanum_lycopersicum", "4081"), ] @@ -62,8 +64,11 @@ def iter_terms(version: str) -> Iterable[Term]: for species_code, taxonomy_id in _PATHWAY_INFO: url = f"{base_url}-{species_code}.gmt" - path = ensure_path(PREFIX, url=url, version=version) - + try: + path = ensure_path(PREFIX, url=url, version=version) + except urllib.error.HTTPError as e: + logger.warning("HTTP %s error when downloading WikiPathways file %s", e.code, url) + continue species_code = species_code.replace("_", " ") taxonomy_name = SPECIES_REMAPPING.get(species_code, species_code)