Added tests for gemini inheritance and gemini queries

tests/plugins/gemini/test_gemini_init.py

@@ -13,7 +13,7 @@ def test_setup_no_db():
  assert adapter.variant_type == 'snv'
 
  assert adapter.filters.can_filter_gene == True
- assert adapter.filters.can_filter_inheritance == False
+ assert adapter.filters.can_filter_inheritance == True
 
 def test_setup_with_variant_type(gemini_path):
  adapter = GeminiPlugin('sv')

tests/plugins/gemini/test_gemini_variant_mixin.py

@@ -241,20 +241,20 @@ def test_filters_range(self, gemini_case_obj):
  assert nr_of_variants == 1
 
 class TestGeminiInheritance:
- def test_filters_ar(self, gemini_large_case_obj):
+ def test_filters_ar(self, gemini_case_obj):
  plugin = GeminiPlugin()
- plugin.add_case(gemini_large_case_obj)
+ plugin.add_case(gemini_case_obj)
 
  filters = {'genetic_models': ['AR_hom']}
  result = plugin.variants('643594', filters=filters, count=100000)
  variants = result.variants
  nr_of_variants = result.nr_of_variants
 
- assert nr_of_variants == 635
+ assert nr_of_variants == 0
 
- def test_filters_ad(self, gemini_large_case_obj):
+ def test_filters_ad(self, gemini_case_obj):
  plugin = GeminiPlugin()
- plugin.add_case(gemini_large_case_obj)
+ plugin.add_case(gemini_case_obj)
 
  filters = {'genetic_models': ['AD']}
  result = plugin.variants('643594', filters=filters, count=1000)
@@ -263,24 +263,24 @@ def test_filters_ad(self, gemini_large_case_obj):
 
  assert nr_of_variants == 0
 
- def test_filters_ad_dn(self, gemini_large_case_obj):
+ def test_filters_ad_dn(self, gemini_case_obj):
  plugin = GeminiPlugin()
- plugin.add_case(gemini_large_case_obj)
+ plugin.add_case(gemini_case_obj)
 
  filters = {'genetic_models': ['AD_dn']}
  result = plugin.variants('643594', filters=filters, count=1000)
  variants = result.variants
  nr_of_variants = result.nr_of_variants
 
- assert nr_of_variants == 170
+ assert nr_of_variants == 6
 
- def test_filters_ar_comp(self, gemini_large_case_obj):
+ def test_filters_ar_comp(self, gemini_case_obj):
  plugin = GeminiPlugin()
- plugin.add_case(gemini_large_case_obj)
+ plugin.add_case(gemini_case_obj)
 
  filters = {'genetic_models': ['AR_comp']}
  result = plugin.variants('643594', filters=filters, count=10000)
  variants = result.variants
  nr_of_variants = result.nr_of_variants
 
- assert nr_of_variants == 2466
+ assert nr_of_variants == 0

tests/utils/test_gemini_query.py

@@ -0,0 +1,36 @@
+from puzzle.utils.gemini_extras import (add_to_query, build_gemini_query)
+
+def test_add_to_query():
+ query = "SELECT * from variants"
+ extra_info = "max_aaf_all < 0.01"
+ new_query = add_to_query(query, extra_info)
+ assert new_query == "SELECT * from variants WHERE max_aaf_all < 0.01"
+
+ extra_info = "cadd_score > 10"
+ new_query = add_to_query(new_query, extra_info)
+ assert new_query == "SELECT * from variants WHERE max_aaf_all < 0.01 AND cadd_score > 10"
+
+def test_build_gemini_query():
+ filters = {
+ 'frequency' : 0.01
+ }
+ query = build_gemini_query(filters)
+
+ assert query == "SELECT * from variants WHERE (max_aaf_all < 0.01 or max_aaf_all is Null)"
+
+def test_build_gemini_query_models():
+ filters = {
+ 'frequency' : 0.01
+ }
+ query = build_gemini_query(filters, add_where = False)
+
+ assert query == "(max_aaf_all < 0.01 or max_aaf_all is Null)"
+
+def test_build_gemini_query_models_two():
+ filters = {
+ 'frequency' : 0.01,
+ 'cadd' : 15.0
+ }
+ query = build_gemini_query(filters, add_where = False)
+
+ assert query == "(max_aaf_all < 0.01 or max_aaf_all is Null) AND (cadd_scaled > 15.0)"