chore: move VariationNormalizerRESTDataProxy to notebooks

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)"
    ]

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",

src/ga4gh/vrs/extras/variation_normalizer_rest_dp.py → 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)