From 9b58c5cf3eb5aa21399679c8049bd09d2f67d05c Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Tue, 26 Mar 2024 13:36:03 -0400
Subject: [PATCH] chore: move VariationNormalizerRESTDataProxy to notebooks

* This dp is only for notebooks, so it should live within the notebook
  dir
---
 notebooks/Extras.ipynb                         |  2 +-
 notebooks/HGVS Translation.ipynb               |  6 +++---
 .../variation_normalizer_rest_dp.py            | 14 ++++++--------
 .../test_variation_normalizer_rest_dp.py       | 18 ------------------
 4 files changed, 10 insertions(+), 30 deletions(-)
 rename {src/ga4gh/vrs/extras => notebooks}/variation_normalizer_rest_dp.py (71%)
 delete mode 100644 tests/extras/test_variation_normalizer_rest_dp.py

diff --git a/notebooks/Extras.ipynb b/notebooks/Extras.ipynb
index 0bb04b88..209a8f16 100644
--- a/notebooks/Extras.ipynb
+++ b/notebooks/Extras.ipynb
@@ -210,7 +210,7 @@
     }
    ],
    "source": [
-    "from ga4gh.vrs.extras.variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy\n",
+    "from variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy\n",
     "vnorm = VariationNormalizerRESTDataProxy()\n",
     "vnorm.to_hgvs(a)"
    ]
diff --git a/notebooks/HGVS Translation.ipynb b/notebooks/HGVS Translation.ipynb
index 7d0052d5..a1a0b128 100644
--- a/notebooks/HGVS Translation.ipynb	
+++ b/notebooks/HGVS Translation.ipynb	
@@ -287,7 +287,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ga4gh.vrs.extras.variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy\n",
+    "from variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy\n",
     "vnorm = VariationNormalizerRESTDataProxy()"
    ]
   },
@@ -423,10 +423,10 @@
    "source": [
     "import tabulate\n",
     "from ga4gh.vrs.normalize import normalize\n",
-    "from ga4gh.vrs.extras.variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy\n",
+    "from variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy\n",
     "vnorm = VariationNormalizerRESTDataProxy()\n",
     "\n",
-    "#The postgres default port of 5432 is blocked outbound by binder and potentially other institutions. \n",
+    "#The postgres default port of 5432 is blocked outbound by binder and potentially other institutions.\n",
     "#To circumvent users having to install UTA themsleves we created a rest data proxy for variation normalizer for the to_hgvs endpoint.\n",
     "\n",
     "# todo: this example should get changed to use normalized hgvs_g as input.\n",
diff --git a/src/ga4gh/vrs/extras/variation_normalizer_rest_dp.py b/notebooks/variation_normalizer_rest_dp.py
similarity index 71%
rename from src/ga4gh/vrs/extras/variation_normalizer_rest_dp.py
rename to notebooks/variation_normalizer_rest_dp.py
index 14dd6ddc..44f4c604 100644
--- a/src/ga4gh/vrs/extras/variation_normalizer_rest_dp.py
+++ b/notebooks/variation_normalizer_rest_dp.py
@@ -1,18 +1,16 @@
 import requests
 
 class VariationNormalizerRESTDataProxy:
-    """
-    Rest data proxy for Variation Normalizer API
-    """
+    """Rest data proxy for Variation Normalizer API"""
     def __init__(self) -> None:
         """
         Initialize class with the API URL
         """
         self.api = "https://normalize.cancervariants.org/variation"
 
-    def to_hgvs(self, vo, namespace="refseq"):
-        """
-        tranlsate vrs allele object (vo) to hgvs format
+    def to_hgvs(self, vo, namespace="refseq") -> list[str]:
+        """Translate vrs allele object (vo) to hgvs format
+
         Use this method if you don't have UTA installed locally or are unable
         to reach the public UTA database due to port issues.
         """
@@ -29,5 +27,5 @@ def to_hgvs(self, vo, namespace="refseq"):
         if r.status_code == 200:
             return r.json().get("variations", [])
         else:
-            raise requests.HTTPError(f"Variation normalizer returned the status code: {r.status_code}.")
-
+            err_msg = f"Variation normalizer returned the status code: {r.status_code}."
+            raise requests.HTTPError(err_msg)
diff --git a/tests/extras/test_variation_normalizer_rest_dp.py b/tests/extras/test_variation_normalizer_rest_dp.py
deleted file mode 100644
index 03aad933..00000000
--- a/tests/extras/test_variation_normalizer_rest_dp.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import pytest
-
-from ga4gh.vrs import models
-from ga4gh.vrs.extras.variation_normalizer_rest_dp import VariationNormalizerRESTDataProxy
-from tests.extras.test_allele_translator import hgvs_tests, hgvs_tests_to_hgvs_map
-
-
-@pytest.fixture(scope="module")
-def variation_norm_rest_dp():
-    return VariationNormalizerRESTDataProxy()
-
-
-@pytest.mark.parametrize("expected,vo_as_dict", hgvs_tests)
-@pytest.mark.vcr
-def test_rest_dp_to_hgvs(variation_norm_rest_dp, expected, vo_as_dict):
-    vo = models.Allele(**vo_as_dict)
-    resp = variation_norm_rest_dp.to_hgvs(vo)
-    assert resp == [hgvs_tests_to_hgvs_map.get(expected, expected)]