From 3a9c486925864f68b990a24896def6439c7d5aec Mon Sep 17 00:00:00 2001
From: james stevenson <james.stevenson@nationwidechildrens.org>
Date: Sun, 3 Oct 2021 18:29:47 -0400
Subject: [PATCH] Add OncoTree (#20)

* Add initial OncoTree getter

* Add oncotree homepage

* linting fixes

Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com>
---
 src/bioversions/sources/__init__.py |  2 ++
 src/bioversions/sources/oncotree.py | 40 +++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 src/bioversions/sources/oncotree.py

diff --git a/src/bioversions/sources/__init__.py b/src/bioversions/sources/__init__.py
index ab8be248..a8919e41 100644
--- a/src/bioversions/sources/__init__.py
+++ b/src/bioversions/sources/__init__.py
@@ -33,6 +33,7 @@
 from .npass import NPASSGetter
 from .obo import iter_obo_getters
 from .ols import extend_ols_getters
+from .oncotree import OncoTreeGetter
 from .pathbank import PathBankGetter
 from .pfam import PfamGetter
 from .pombase import PombaseGetter
@@ -94,6 +95,7 @@ def get_getters() -> List[Type[Getter]]:
         NCItGetter,
         RxNormGetter,
         ChemIDplusGetter,
+        OncoTreeGetter,
         MOAlmanacGetter,
     ]
     getters.extend(iter_obo_getters())
diff --git a/src/bioversions/sources/oncotree.py b/src/bioversions/sources/oncotree.py
new file mode 100644
index 00000000..bb4c6995
--- /dev/null
+++ b/src/bioversions/sources/oncotree.py
@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for OncoTree."""
+
+import requests
+
+from ..utils import Getter, VersionType
+
+
+__all__ = [
+    "OncoTreeGetter",
+]
+
+
+class OncoTreeGetter(Getter):
+    """A getter for OncoTree."""
+
+    bioregistry_id = "oncotree"
+    name = "OncoTree"
+    homepage_fmt = "http://oncotree.mskcc.org/api/tumorTypes?version=oncotree_{version}"
+    version_type = VersionType.date
+    date_version_fmt = "%Y-%m-%d"
+
+    def get(self) -> str:
+        """Get the latest OncoTree version number."""
+        res = requests.get("http://oncotree.mskcc.org/api/versions", params={"format": "json"})
+        res_json = res.json()
+        version = next(
+            (r["release_date"] for r in res_json if r["api_identifier"] == "oncotree_latest_stable")
+        )
+        return version
+
+    @staticmethod
+    def homepage_version_transform(version: str) -> str:
+        """Reformat version value for OncoTree data URL."""
+        return version.replace("-", "_")
+
+
+if __name__ == "__main__":
+    OncoTreeGetter.print()