From 24442211ec711b7b5cf0add0abb6e1521bd99a5e Mon Sep 17 00:00:00 2001
From: Lauren Rekerle <lauren.rekerle@jax.org>
Date: Wed, 24 Jul 2024 11:54:26 -0500
Subject: [PATCH] Small changes to variant formatter

---
 src/genophenocorr/view/_formatter.py |  5 ++---
 tests/model/test_variant.py          | 27 +--------------------------
 tests/view/test_formatter.py         | 24 ++++++++++++++++++++++++
 3 files changed, 27 insertions(+), 29 deletions(-)
 create mode 100644 tests/view/test_formatter.py

diff --git a/src/genophenocorr/view/_formatter.py b/src/genophenocorr/view/_formatter.py
index a9a225bf..dab9f971 100644
--- a/src/genophenocorr/view/_formatter.py
+++ b/src/genophenocorr/view/_formatter.py
@@ -13,8 +13,7 @@ def format_as_string(self, item: T) -> str:
         to more easily read the item in tables or other visualizers.
 
         Args:
-            item (T): a genophenocorr class
-            tx_id (typing.Optional[str]): The desired transcript ID, if not the MANE transcript
+            item (T): an element to be formatted
 
         Returns:
             str: a human readable string 
@@ -32,7 +31,6 @@ def format_as_string(self, item: Variant) -> str:
         """ 
         Args:
             item (Variant): An object of class `Variant` representing a variant.
-            tx_id (typing.Optional[str]): The transcript ID, needed if using a transcript other than the MANE transcript.
 
         Returns:
             str: A human readable string for the variant.
@@ -48,4 +46,5 @@ def format_as_string(self, item: Variant) -> str:
         elif item.variant_coordinates.variant_key is not None:
             return item.variant_coordinates.variant_key
         else:
+            # To be reevaluated
             return f"Variant {item} has no string format."
\ No newline at end of file
diff --git a/tests/model/test_variant.py b/tests/model/test_variant.py
index c6f8329c..484bbd6a 100644
--- a/tests/model/test_variant.py
+++ b/tests/model/test_variant.py
@@ -3,17 +3,8 @@
 import typing
 
 from genophenocorr.model import Variant, Cohort
-from genophenocorr.view import VariantFormatter
-
 
 class TestVariant:
-    
-    @pytest.fixture
-    def test_cohort(
-        self, 
-        suox_cohort: Cohort
-    ) -> Cohort:
-        return suox_cohort
 
     @pytest.fixture
     def some_variant(
@@ -36,20 +27,4 @@ def test_get_hgvs_cdna_by_tx(
     ):
         hgvs = some_variant.get_hgvs_cdna_by_tx_id(transcript_id=tx_id)
 
-        assert hgvs == expected
-        
-    @pytest.mark.parametrize(
-        "variant, expected",
-        [
-            ('12_56004525_56004525_A_G', "NM_001032386.2:c.1136A>G"),
-        ]
-    )
-    def test_variant_formatter(
-        self, 
-        variant: str,
-        expected: str,
-        test_cohort: Cohort
-    ):
-        var = test_cohort.get_variant_by_key(variant)
-        formatter = VariantFormatter()
-        assert formatter.format_as_string(var) == expected
+        assert hgvs == expected
\ No newline at end of file
diff --git a/tests/view/test_formatter.py b/tests/view/test_formatter.py
new file mode 100644
index 00000000..45842a2c
--- /dev/null
+++ b/tests/view/test_formatter.py
@@ -0,0 +1,24 @@
+import pytest
+
+import typing
+
+from genophenocorr.model import Cohort
+from genophenocorr.view import VariantFormatter
+
+class TestFormatter:
+    
+    @pytest.mark.parametrize(
+        "variant, expected",
+        [
+            ('12_56004525_56004525_A_G', "NM_001032386.2:c.1136A>G"),
+        ]
+    )
+    def test_variant_formatter(
+        self, 
+        variant: str,
+        expected: str,
+        suox_cohort: Cohort
+    ):
+        var = suox_cohort.get_variant_by_key(variant)
+        formatter = VariantFormatter()
+        assert formatter.format_as_string(var) == expected
\ No newline at end of file