From aa9011e1a1bbaa80d22cfaa8173cf5bdceef5132 Mon Sep 17 00:00:00 2001
From: moonso <monsunas@gmail.com>
Date: Fri, 29 Apr 2016 09:24:28 +0200
Subject: [PATCH] Added tests for gemini inheritance and gemini queries

---
 tests/plugins/gemini/test_gemini_init.py      |  2 +-
 .../gemini/test_gemini_variant_mixin.py       | 22 ++++++------
 tests/utils/test_gemini_query.py              | 36 +++++++++++++++++++
 3 files changed, 48 insertions(+), 12 deletions(-)
 create mode 100644 tests/utils/test_gemini_query.py

diff --git a/tests/plugins/gemini/test_gemini_init.py b/tests/plugins/gemini/test_gemini_init.py
index f8d748b..a913c44 100644
--- a/tests/plugins/gemini/test_gemini_init.py
+++ b/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')
diff --git a/tests/plugins/gemini/test_gemini_variant_mixin.py b/tests/plugins/gemini/test_gemini_variant_mixin.py
index 158d360..1dfa551 100644
--- a/tests/plugins/gemini/test_gemini_variant_mixin.py
+++ b/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
diff --git a/tests/utils/test_gemini_query.py b/tests/utils/test_gemini_query.py
new file mode 100644
index 0000000..d2b1b1c
--- /dev/null
+++ b/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)"
\ No newline at end of file