From 33d5aadec28923563453fe6d0ee299d29a301701 Mon Sep 17 00:00:00 2001
From: joeflack4 <joeflack4@gmail.com>
Date: Tue, 18 Oct 2022 18:17:58 -0400
Subject: [PATCH] OWL to FHIR - Add: New converter for OWL to FHIR CodeSystem
 JON (WIP) - Add: Tests for new converter (WIP)

Misc
- Update: .gitignore: added: .DS_Store
---
 .gitignore                                |  4 +---
 src/oaklib/converters/owl_to_fhir.py      | 25 +++++++++++++++++++++++
 tests/test_converters/test_owl_to_fhir.py | 18 ++++++++++++++++
 3 files changed, 44 insertions(+), 3 deletions(-)
 create mode 100644 src/oaklib/converters/owl_to_fhir.py
 create mode 100644 tests/test_converters/test_owl_to_fhir.py

diff --git a/.gitignore b/.gitignore
index ab19e7a16..766c51667 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,12 +13,10 @@ db/
 notebooks/output/*json
 notebooks/output/*tsv
 notebooks/input/*
-
-
 notebooks/api-key.txt
 
 .template.db
 .venv
 .tox/
 .coverage.*
-
+.DS_Store
diff --git a/src/oaklib/converters/owl_to_fhir.py b/src/oaklib/converters/owl_to_fhir.py
new file mode 100644
index 000000000..78b41b7a3
--- /dev/null
+++ b/src/oaklib/converters/owl_to_fhir.py
@@ -0,0 +1,25 @@
+"""Convert OWL to FHIR CodeSystem JSON
+
+TODO's
+  1. Write functioning converter
+  2. Optional/Later: Schema mappings (Obograph -> FHIR CodeSystem). SchemaAutomator? Other approach?
+  3. Add converter to CLI
+  4. Test(s)
+
+todo's (minor)
+  1. owl_to_fhir.py -> owl_to_fhir_codesystem.py?
+"""
+from typing import Dict
+
+
+def convert(inpath: str, outpath: str) -> Dict:
+	"""Convert
+
+	Side effects:
+	- Writes file at `outpath`"""
+
+	return {}
+
+
+if __name__ == '__main__':
+	convert('path/to/mondo-example.owl')
diff --git a/tests/test_converters/test_owl_to_fhir.py b/tests/test_converters/test_owl_to_fhir.py
new file mode 100644
index 000000000..b5e6355e1
--- /dev/null
+++ b/tests/test_converters/test_owl_to_fhir.py
@@ -0,0 +1,18 @@
+"""Tests for OWL to FHIR CodeSystem converter."""
+import unittest
+
+from oaklib.converters.owl_to_fhir import convert
+from tests import INPUT_DIR, OUTPUT_DIR
+
+
+ONT = INPUT_DIR / "mondo-example.owl"
+OUT = OUTPUT_DIR / "mondo-example.json"
+
+
+class OwlToFhirConversionTest(unittest.TestCase):
+    """Tests"""
+
+    def test_convert(self):
+        """Tests basic conversion"""
+        result = convert(ONT)
+        self.assertTrue(result != True)  # todo