feat: add NCBI gene summary artifact

src/wags_tails/__init__.py

@@ -18,6 +18,7 @@
 from wags_tails.moa import MoaData
 from wags_tails.mondo import MondoData
 from wags_tails.ncbi import NcbiGeneData, NcbiGenomeData
+from wags_tails.ncbi_gene_summary import NcbiGeneSummaryData
 from wags_tails.ncbi_lrg_refseqgene import NcbiLrgRefSeqGeneData
 from wags_tails.ncbi_mane import NcbiManeRefSeqGenomicData, NcbiManeSummaryData
 from wags_tails.ncit import NcitData
@@ -48,6 +49,7 @@
     "MoaData",
     "MondoData",
     "NcbiGeneData",
+    "NcbiGeneSummaryData",
     "NcbiGenomeData",
     "NcbiLrgRefSeqGeneData",
     "NcbiManeRefSeqGenomicData",

src/wags_tails/ncbi_gene_summary.py

@@ -0,0 +1,32 @@
+"""Get NCBI gene summary file
+
+Updated daily at https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_summary.gz
+
+See https://ftp.ncbi.nlm.nih.gov/gene/DATA/README for more info
+"""
+
+from datetime import UTC, datetime
+from pathlib import Path
+
+from wags_tails.base_source import DataSource
+from wags_tails.utils.downloads import download_http, handle_gzip
+from wags_tails.utils.versioning import DATE_VERSION_PATTERN
+
+
+class NcbiGeneSummaryData(DataSource):
+    """Provide access to NCBI gene_summary file"""
+
+    _src_name = "ncbi_gene_summary"
+    _filetype = "tsv"
+
+    def _get_latest_version(self) -> str:
+        return datetime.now(UTC).strftime(DATE_VERSION_PATTERN)
+
+    def _download_data(self, version: str, outfile: Path) -> None:  # noqa: ARG002
+        """Download data file to specified location.
+
+        :param version: version to acquire
+        :param outfile: location and filename for final data file
+        """
+        url = "https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_summary.gz"
+        download_http(url, outfile, handler=handle_gzip, tqdm_params=self._tqdm_params)

tests/test_ncbi_gene_summary.py

@@ -0,0 +1,77 @@
+"""Test NCBI gene summary data source."""
+
+import json
+from datetime import UTC, datetime
+from pathlib import Path
+
+import pytest
+import requests_mock
+
+from wags_tails import NcbiGeneSummaryData
+
+
+@pytest.fixture
+def ncbi_gs_data_dir(base_data_dir: Path):
+    """Provide fixture for ncbi gene summary wags-tails directory"""
+    directory = base_data_dir / "ncbi_gene_summary"
+    directory.mkdir(exist_ok=True, parents=True)
+    return directory
+
+
+@pytest.fixture
+def ncbi_gs(ncbi_gs_data_dir: Path):
+    """Provide fixture for fetcher instance"""
+    return NcbiGeneSummaryData(ncbi_gs_data_dir, silent=True)
+
+
+@pytest.fixture(scope="module")
+def info_response(fixture_dir):
+    """Provide fixture for ncbi website release info response"""
+    with (fixture_dir / "gene_summary.gz").open() as f:
+        return json.load(f)
+
+
+@pytest.fixture(scope="module")
+def ncbi_gs_file(fixture_dir):
+    """Provide fixture for HGNC data file"""
+    with (fixture_dir / "gene_summary.gz").open("rb") as f:
+        return f.read()
+
+
+def test_get_latest(
+    ncbi_gs: NcbiGeneSummaryData,
+    ncbi_gs_data_dir: Path,
+    ncbi_gs_file: bytes,
+    monkeypatch,
+):
+    with pytest.raises(
+        ValueError, match="Cannot set both `force_refresh` and `from_local`"
+    ):
+        ncbi_gs.get_latest(from_local=True, force_refresh=True)
+
+    with pytest.raises(FileNotFoundError):
+        ncbi_gs.get_latest(from_local=True)
+
+    class MockDateTime(datetime):
+        @classmethod
+        def now(cls, tz=None):  # noqa: ARG003
+            return datetime(2026, 1, 1, tzinfo=UTC)
+
+    monkeypatch.setattr("wags_tails.ncbi_gene_summary.datetime", MockDateTime)
+
+    with requests_mock.Mocker() as m:
+        m.get(
+            "https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_summary.gz",
+            content=ncbi_gs_file,
+        )
+        path, version = ncbi_gs.get_latest()
+        assert path == ncbi_gs_data_dir / "ncbi_gene_summary_20260101.tsv"
+        assert path.exists()
+        assert version == "20260101"
+        assert m.call_count == 1
+
+        path, version = ncbi_gs.get_latest()
+        assert path == ncbi_gs_data_dir / "ncbi_gene_summary_20260101.tsv"
+        assert path.exists()
+        assert version == "20260101"
+        assert m.call_count == 1