From 71a688a4a04295429c6c4ae6044f79fc81674b47 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 24 Apr 2026 11:56:48 -0400
Subject: [PATCH 1/3] feat: add ncbi gene summary

---
 src/wags_tails/__init__.py          |   2 +
 src/wags_tails/base_source.py       |  15 +++---
 src/wags_tails/ncbi_gene_summary.py |  32 ++++++++++++
 tests/fixtures/gene_summary.gz      | Bin 0 -> 626 bytes
 tests/test_ncbi_gene_summary.py     |  77 ++++++++++++++++++++++++++++
 5 files changed, 119 insertions(+), 7 deletions(-)
 create mode 100644 src/wags_tails/ncbi_gene_summary.py
 create mode 100644 tests/fixtures/gene_summary.gz
 create mode 100644 tests/test_ncbi_gene_summary.py

diff --git a/src/wags_tails/__init__.py b/src/wags_tails/__init__.py
index d9d4b47..69923e1 100644
--- a/src/wags_tails/__init__.py
+++ b/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",
diff --git a/src/wags_tails/base_source.py b/src/wags_tails/base_source.py
index f6f4ccc..1e5c48b 100644
--- a/src/wags_tails/base_source.py
+++ b/src/wags_tails/base_source.py
@@ -31,7 +31,7 @@ class DataSource(abc.ABC):
 
     # required attributes
     _src_name: str
-    _filetype: str
+    _filetype: str | None
     _versioned: bool = True
 
     def __init__(self, data_dir: Path | None = None, silent: bool = True) -> None:
@@ -89,15 +89,16 @@ def get_latest(
             msg = "Cannot set both `force_refresh` and `from_local`"
             raise ValueError(msg)
 
+        filetype_suffix = f".{self._filetype}" if self._filetype else ""
         if from_local:
             file_glob = (
-                f"{self._src_name}_*.{self._filetype}"
+                f"{self._src_name}_*{filetype_suffix}"
                 if self._versioned
-                else f"{self._src_name}.{self._filetype}"
+                else f"{self._src_name}{filetype_suffix}"
             )
             file_path = get_latest_local_file(self.data_dir, file_glob)
             version = (
-                parse_file_version(file_path, f"{self._src_name}_(.+).{self._filetype}")
+                parse_file_version(file_path, f"{self._src_name}_(.+){filetype_suffix}")
                 if self._versioned
                 else ""
             )
@@ -105,16 +106,16 @@ def get_latest(
 
         latest_version = self._get_latest_version()
         latest_file = (
-            f"{self._src_name}_{latest_version}.{self._filetype}"
+            f"{self._src_name}_{latest_version}{filetype_suffix}"
             if self._versioned
-            else f"{self._src_name}.{self._filetype}"
+            else f"{self._src_name}{filetype_suffix}"
         )
         latest_file_path = self.data_dir / latest_file
         if (not force_refresh) and latest_file_path.exists():
             _logger.debug(
                 "Found existing file, %s, matching latest version %s.",
                 latest_file_path.name,
-                latest_version if latest_version else "(unversioned)",
+                latest_version or "(unversioned)",
             )
             return latest_file_path, latest_version
         self._download_data(latest_version, latest_file_path)
diff --git a/src/wags_tails/ncbi_gene_summary.py b/src/wags_tails/ncbi_gene_summary.py
new file mode 100644
index 0000000..166c3a6
--- /dev/null
+++ b/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)
diff --git a/tests/fixtures/gene_summary.gz b/tests/fixtures/gene_summary.gz
new file mode 100644
index 0000000000000000000000000000000000000000..da639f5cc5bda68cc216e31e3aa8c2b06ab39410
GIT binary patch
literal 626
zcmV-&0*(D2iwFo&z3OQI17~G!WnXi3ZEaz4c>wKGyOP^546L26Kxt=A9^1K$<1&+L
z+@$cO%cP(vSi%eiG9cwU-`59}{JP{1VpWnT5ZGPpuGY)tWVv`;Z$51v*OMLYpYivk
zB`bdS{cD72OZhniBM7nal3==86st$zGz0crSYHv>&{wC%q`s2);N1Z$eSzR(Dv}tE
zRwyL$Y#a#Ioiq6Z{2pp#1bhvGG3Fz^)pjnCMd!3kz)NkIVjH16g4yrUraZLtsnMZ|
zESZuVCH=`2^uw;*+l*}v1Ct)!8BM7OwV|FXN_T8gOhnjj!9)l~x$13eLeR3@H`ka7
z`KZ11C<wJij&S9sdg)<t)~uJq8irEYk>V7+;}g<FH7_?B&f$kr`L`=j1nbZo2DF*)
zlla&ePzIj6{I7?-1>`qn0m<h<RcBFggAx$`s$CPhBdiw%Clw6a!g(LG5N#(>k@T=L
z0~{F49^j=R+vNHCPI~-*;jqW#gELVL15dgxc@If(<kgB!?#mTIr}7VjvZ96)MdWxs
z(>=<`b023X4k-@8yt}NBh^?34rQZdy&N6wE1#u=`K_rK4v&z=D!Qm@RciZQ07goyK
z*GzAyzBN)~8jPYq#do!`ZUaho8kCt!FeJIz3!OZ7Wznj`^N`lF3alnp?`C|rMpVxe
zH&oK#N`VSbrhU5@HFv#%GSD6(sa<nAkW=i-^rIr1nV++IUFjTts&WUaPVVj-Jis#s
zSS=QtUmsStq5m?5ehmE>`uhs~W(@rp`Z4r(75dMMG4x~T$I#zb=$B*Y$Iy?V|L;Tp
M2Nz`<lF1VQ0BiU)UH||9

literal 0
HcmV?d00001

diff --git a/tests/test_ncbi_gene_summary.py b/tests/test_ncbi_gene_summary.py
new file mode 100644
index 0000000..be14639
--- /dev/null
+++ b/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

From 9da3fdacd5001f1339ef79365033b334de7acfa9 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 24 Apr 2026 12:35:40 -0400
Subject: [PATCH 2/3] rm

---
 src/wags_tails/base_source.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/wags_tails/base_source.py b/src/wags_tails/base_source.py
index 1e5c48b..db88b95 100644
--- a/src/wags_tails/base_source.py
+++ b/src/wags_tails/base_source.py
@@ -31,7 +31,7 @@ class DataSource(abc.ABC):
 
     # required attributes
     _src_name: str
-    _filetype: str | None
+    _filetype: str
     _versioned: bool = True
 
     def __init__(self, data_dir: Path | None = None, silent: bool = True) -> None:

From e1ada81cce73d157f5dd5c9bb833184e933bfc0b Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 24 Apr 2026 12:36:09 -0400
Subject: [PATCH 3/3] revert

---
 src/wags_tails/base_source.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/wags_tails/base_source.py b/src/wags_tails/base_source.py
index db88b95..f6f4ccc 100644
--- a/src/wags_tails/base_source.py
+++ b/src/wags_tails/base_source.py
@@ -89,16 +89,15 @@ def get_latest(
             msg = "Cannot set both `force_refresh` and `from_local`"
             raise ValueError(msg)
 
-        filetype_suffix = f".{self._filetype}" if self._filetype else ""
         if from_local:
             file_glob = (
-                f"{self._src_name}_*{filetype_suffix}"
+                f"{self._src_name}_*.{self._filetype}"
                 if self._versioned
-                else f"{self._src_name}{filetype_suffix}"
+                else f"{self._src_name}.{self._filetype}"
             )
             file_path = get_latest_local_file(self.data_dir, file_glob)
             version = (
-                parse_file_version(file_path, f"{self._src_name}_(.+){filetype_suffix}")
+                parse_file_version(file_path, f"{self._src_name}_(.+).{self._filetype}")
                 if self._versioned
                 else ""
             )
@@ -106,16 +105,16 @@ def get_latest(
 
         latest_version = self._get_latest_version()
         latest_file = (
-            f"{self._src_name}_{latest_version}{filetype_suffix}"
+            f"{self._src_name}_{latest_version}.{self._filetype}"
             if self._versioned
-            else f"{self._src_name}{filetype_suffix}"
+            else f"{self._src_name}.{self._filetype}"
         )
         latest_file_path = self.data_dir / latest_file
         if (not force_refresh) and latest_file_path.exists():
             _logger.debug(
                 "Found existing file, %s, matching latest version %s.",
                 latest_file_path.name,
-                latest_version or "(unversioned)",
+                latest_version if latest_version else "(unversioned)",
             )
             return latest_file_path, latest_version
         self._download_data(latest_version, latest_file_path)