From ec13d897e02121782eb75c5626fab7508b2cf846 Mon Sep 17 00:00:00 2001 From: wayne-monical Date: Sun, 1 Jun 2025 14:52:53 -0400 Subject: [PATCH 1/2] fixing url thanks to https://github.com/statgen/pheweb/commit/84cda612afdf72133bed210b46d8a2f35d0f98df --- pheweb/load/make_gene_aliases_sqlite3.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pheweb/load/make_gene_aliases_sqlite3.py b/pheweb/load/make_gene_aliases_sqlite3.py index 530c80786..5f5485c6e 100644 --- a/pheweb/load/make_gene_aliases_sqlite3.py +++ b/pheweb/load/make_gene_aliases_sqlite3.py @@ -11,7 +11,8 @@ def get_genenamesorg_ensg_aliases_map(ensgs_to_consider: Iterable[str]) -> Dict[str, List[str]]: ensgs_to_consider = set(ensgs_to_consider) - r = urllib.request.urlopen('http://ftp.ebi.ac.uk/pub/databases/genenames/new/json/non_alt_loci_set.json') + # r = urllib.request.urlopen('http://ftp.ebi.ac.uk/pub/databases/genenames/new/json/non_alt_loci_set.json') + r = urllib.request.urlopen('https://storage.googleapis.com/public-download-files/hgnc/json/json/non_alt_loci_set.json') data = r.read().decode('utf-8') ensg_to_aliases = {} for row in json.loads(data)['response']['docs']: From 54782cfc2598ea1cf12ea53d6a11e70d7b250337 Mon Sep 17 00:00:00 2001 From: Wayne Monical Date: Tue, 5 Aug 2025 14:04:02 -0400 Subject: [PATCH 2/2] fixing url 2nd try --- pheweb/load/make_gene_aliases_sqlite3.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pheweb/load/make_gene_aliases_sqlite3.py b/pheweb/load/make_gene_aliases_sqlite3.py index 5f5485c6e..da845c91c 100644 --- a/pheweb/load/make_gene_aliases_sqlite3.py +++ b/pheweb/load/make_gene_aliases_sqlite3.py @@ -11,8 +11,8 @@ def get_genenamesorg_ensg_aliases_map(ensgs_to_consider: Iterable[str]) -> Dict[str, List[str]]: ensgs_to_consider = set(ensgs_to_consider) - # r = urllib.request.urlopen('http://ftp.ebi.ac.uk/pub/databases/genenames/new/json/non_alt_loci_set.json') - r = urllib.request.urlopen('https://storage.googleapis.com/public-download-files/hgnc/json/json/non_alt_loci_set.json') + r = urllib.request.urlopen('https://ftp.ebi.ac.uk/pub/databases/genenames/out_of_date_hgnc/json/non_alt_loci_set.json') + data = r.read().decode('utf-8') ensg_to_aliases = {} for row in json.loads(data)['response']['docs']: