From d714260914aefe7ede3bccb050f203280fbeb404 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Tue, 22 Oct 2024 08:17:32 -0500
Subject: [PATCH] For variants, implement a subtype property to easier identify
 the type of variant

---
 civicpy/civic.py            | 17 +++++++++++------
 civicpy/tests/test_civic.py |  6 ++++++
 civicpy/utils.py            | 10 +++-------
 3 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/civicpy/civic.py b/civicpy/civic.py
index c870955..791ce1e 100644
--- a/civicpy/civic.py
+++ b/civicpy/civic.py
@@ -505,6 +505,7 @@ def sanitized_name(self):
 
 class Variant(CivicRecord):
     _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({
+        'subtype',
         'feature_id',
         'name',
         'single_variant_molecular_profile_id',
@@ -524,6 +525,9 @@ def __init__(self, **kwargs):
         self._molecular_profiles = []
         super().__init__(**kwargs)
 
+    def __repr__(self):
+        return '<CIViC {} ({}) {}>'.format(self.type, self.subtype, self.id)
+
     @property
     def aliases(self):
         return self.variant_aliases
@@ -1341,7 +1345,10 @@ def _get_elements_by_ids(element, id_list=[], allow_cached=True, get_all=False):
     ids = []
     for e in response_elements:
         e = _postprocess_response_element(e, element)
-        cls = get_class(e['type'])
+        if element == 'variant':
+            cls = get_class(e['subtype'])
+        else:
+            cls = get_class(e['type'])
         partial_element = cls(**e, partial=True)
         ids.append(e['id'])
         elements.append(partial_element)
@@ -1375,9 +1382,9 @@ def _postprocess_response_element(e, element):
         e['variant_ids'] = [v['id'] for v in e['variants']]
         del e['variants']
     elif element == 'variant':
-        e['type'] = e['__typename']
         e['feature_id'] = e['feature']['id']
         if e['__typename'] == 'GeneVariant':
+            e['subtype'] = 'gene_variant'
             e['entrez_id'] = e['feature']['featureInstance']['entrezId']
             e['entrez_name'] = e['feature']['name']
             build = e['coordinates']['reference_build']
@@ -1387,11 +1394,9 @@ def _postprocess_response_element(e, element):
                 build = 'GRCh38'
             e['coordinates']['reference_build'] = build
         elif e['__typename'] == 'FactorVariant':
-            #nothing special to handle
-            pass
+            e['subtype'] = 'factor_variant'
         elif e['__typename'] == 'FusionVariant':
-            #nothing special to handle
-            pass
+            e['subtype'] = 'fusion_variant'
         else:
             raise Exception("Variant type {} not supported yet".format(e['__typename']))
     elif element == 'variant_group':
diff --git a/civicpy/tests/test_civic.py b/civicpy/tests/test_civic.py
index 10539dd..9588363 100644
--- a/civicpy/tests/test_civic.py
+++ b/civicpy/tests/test_civic.py
@@ -160,6 +160,8 @@ class TestGeneVariants(object):
     def test_get_all(self):
         variants = civic.get_all_gene_variants()
         assert len(variants) >= 3557
+        for variant in variants:
+            assert variant.subtype == 'gene_variant'
 
     def test_properties(self):
         variant = civic.get_variant_by_id(11)
@@ -171,6 +173,8 @@ class TestFusionVariants(object):
     def test_get_all(self):
         variants = civic.get_all_fusion_variants()
         assert len(variants) >= 263
+        for variant in variants:
+            assert variant.subtype == 'fusion_variant'
 
     def test_properties(self):
         variant = civic.get_variant_by_id(1)
@@ -182,6 +186,8 @@ class TestFactorVariants(object):
     def test_get_all(self):
         variants = civic.get_all_factor_variants()
         assert len(variants) >= 8
+        for variant in variants:
+            assert variant.subtype == 'factor_variant'
 
     def test_properties(self):
         variant = civic.get_variant_by_id(4985)
diff --git a/civicpy/utils.py b/civicpy/utils.py
index 4716c96..dc30839 100644
--- a/civicpy/utils.py
+++ b/civicpy/utils.py
@@ -24,10 +24,6 @@ def search_url(element, use_search_meta):
 
 
 def snake_to_camel(snake_string):
-    if '_' not in snake_string and any(ele.isupper() for ele in snake_string):
-        #this is already camel case
-        return snake_string
-    else:
-        words = snake_string.split('_')
-        cap_words = [x.capitalize() for x in words]
-        return ''.join(cap_words)
+    words = snake_string.split('_')
+    cap_words = [x.capitalize() for x in words]
+    return ''.join(cap_words)