From a376a64c24dc42aae8b36a54b4a4c63d572b9e77 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Mon, 4 Dec 2023 10:31:29 -0500 Subject: [PATCH] feedback --- src/gene/etl/ensembl.py | 4 ++-- tests/unit/test_ensembl_source.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/gene/etl/ensembl.py b/src/gene/etl/ensembl.py index 33c39357..4a52975a 100644 --- a/src/gene/etl/ensembl.py +++ b/src/gene/etl/ensembl.py @@ -25,7 +25,7 @@ def _extract_data(self, use_existing: bool) -> None: This method is responsible for initializing an instance of a data handler and, in most cases, setting ``self._data_file`` and ``self._version``. - :param bool use_existing: if True, don't try to fetch latest source data + :param use_existing: if True, don't try to fetch latest source data """ self._data_file, raw_version = self._data_source.get_latest( from_local=use_existing @@ -180,7 +180,7 @@ def _add_meta(self) -> None: "/legal/disclaimer.html", version=self._version, data_url={ - "genome_annotations": f"ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.{self._assembly}.{self._version}.gff3.gz" + "genome_annotations": f"ftp://ftp.ensembl.org/pub/release-{self._version}/gff3/homo_sapiens/Homo_sapiens.{self._assembly}.{self._version}.gff3.gz" }, rdp_url=None, data_license_attributes={ diff --git a/tests/unit/test_ensembl_source.py b/tests/unit/test_ensembl_source.py index a3d32183..7660be3e 100644 --- a/tests/unit/test_ensembl_source.py +++ b/tests/unit/test_ensembl_source.py @@ -309,7 +309,7 @@ def test_meta_info(ensembl): ) assert resp.source_meta_.version == "110" assert resp.source_meta_.data_url == { - "genome_annotations": "ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.110.gff3.gz" + "genome_annotations": "ftp://ftp.ensembl.org/pub/release-110/gff3/homo_sapiens/Homo_sapiens.GRCh38.110.gff3.gz" } assert resp.source_meta_.rdp_url is None assert resp.source_meta_.genome_assemblies == ["GRCh38"]