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authorAlexander Kabui2021-04-12 16:53:48 +0300
committerAlexander Kabui2021-04-12 16:53:48 +0300
commit35f5ac0335f44923184ffe0f0a3380a9cf1859ef (patch)
tree8f1fcb15ace3574eb19bd0eafdc5b5bb0822ed09 /tests/unit/computations
parent8ce82f5b6cccc015c38a728864c63c026fe6a3a0 (diff)
parent31ac939f58bf7b6d353ced995ca395376203b25f (diff)
downloadgenenetwork3-35f5ac0335f44923184ffe0f0a3380a9cf1859ef.tar.gz
fix merge conflict
Diffstat (limited to 'tests/unit/computations')
-rw-r--r--tests/unit/computations/test_correlation.py130
1 files changed, 97 insertions, 33 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 631dc18..8f3ef25 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -18,6 +18,8 @@ from gn3.computations.correlations import query_formatter
from gn3.computations.correlations import map_to_mouse_gene_id
from gn3.computations.correlations import compute_all_lit_correlation
from gn3.computations.correlations import compute_all_tissue_correlation
+from gn3.computations.correlations import map_shared_keys_to_values
+from gn3.computations.correlations import process_trait_symbol_dict
class QueryableMixin:
@@ -27,6 +29,10 @@ class QueryableMixin:
"""base method for execute"""
raise NotImplementedError()
+ def cursor(self):
+ """method for creating db cursor"""
+ raise NotImplementedError()
+
def fetchone(self):
"""base method for fetching one iten"""
raise NotImplementedError()
@@ -46,37 +52,39 @@ class IllegalOperationError(Exception):
class DataBase(QueryableMixin):
"""Class for creating db object"""
- def __init__(self):
+ def __init__(self, expected_results=None, password="1234", db_name=None):
+ """expects the expectede results value to be an array"""
+ self.password = password
+ self.db_name = db_name
self.__query_options = None
- self.__results = None
+ self.results_generator(expected_results)
def execute(self, query_options):
"""method to execute an sql query"""
self.__query_options = query_options
- self.results_generator()
+ return 1
+
+ def cursor(self):
+ """method for creating db cursor"""
return self
def fetchone(self):
"""method to fetch single item from the db query"""
if self.__results is None:
- raise IllegalOperationError()
+ return None
return self.__results[0]
def fetchall(self):
"""method for fetching all items from db query"""
if self.__results is None:
- raise IllegalOperationError()
+ return None
return self.__results
- def results_generator(self, expected_results=None):
+ def results_generator(self, expected_results):
"""private method for generating mock results"""
- if expected_results is None:
- self.__results = [namedtuple("lit_coeff", "val")(x*0.1)
- for x in range(1, 4)]
- else:
- self.__results = expected_results
+ self.__results = expected_results
class TestCorrelation(TestCase):
@@ -239,21 +247,23 @@ class TestCorrelation(TestCase):
after doing correlation
"""
- target_trait_lists = [{"gene_id": 15},
- {"gene_id": 17},
- {"gene_id": 11}]
+ target_trait_lists = [("1426679_at", 15),
+ ("1426702_at", 17),
+ ("1426682_at", 11)]
mock_mouse_gene_id.side_effect = [12, 11, 18, 16, 20]
- database_instance = namedtuple("database", "execute")("fetchone")
+ conn = DataBase()
fetch_lit_data.side_effect = [(15, 9), (17, 8), (11, 12)]
lit_results = lit_correlation_for_trait_list(
- database=database_instance, target_trait_lists=target_trait_lists,
+ conn=conn, target_trait_lists=target_trait_lists,
species="rat", trait_gene_id="12")
- expected_results = [{"gene_id": 15, "lit_corr": 9}, {
- "gene_id": 17, "lit_corr": 8}, {"gene_id": 11, "lit_corr": 12}]
+ expected_results = [{"1426679_at": {"gene_id": 15, "lit_corr": 9}},
+ {"1426702_at": {
+ "gene_id": 17, "lit_corr": 8}},
+ {"1426682_at": {"gene_id": 11, "lit_corr": 12}}]
self.assertEqual(lit_results, expected_results)
@@ -262,8 +272,8 @@ class TestCorrelation(TestCase):
the database where the input and mouse geneid are none
"""
- database_instance = DataBase()
- results = fetch_lit_correlation_data(database=database_instance,
+ conn = DataBase()
+ results = fetch_lit_correlation_data(conn=conn,
gene_id="1",
input_mouse_gene_id=None,
mouse_gene_id=None)
@@ -275,10 +285,12 @@ class TestCorrelation(TestCase):
input trait mouse gene id and mouse gene id
"""
- database_instance = DataBase()
+ expected_db_results = [namedtuple("lit_coeff", "val")(x*0.1)
+ for x in range(1, 4)]
+ database_instance = DataBase(expected_results=expected_db_results)
expected_results = ("1", 0.1)
- lit_results = fetch_lit_correlation_data(database=database_instance,
+ lit_results = fetch_lit_correlation_data(conn=database_instance,
gene_id="1",
input_mouse_gene_id="20",
mouse_gene_id="15")
@@ -292,7 +304,7 @@ class TestCorrelation(TestCase):
database_instance = mock.Mock()
database_instance.execute.return_value.fetchone.return_value = None
- lit_results = fetch_lit_correlation_data(database=database_instance,
+ lit_results = fetch_lit_correlation_data(conn=database_instance,
input_mouse_gene_id="12",
gene_id="16",
mouse_gene_id="12")
@@ -345,13 +357,15 @@ class TestCorrelation(TestCase):
database_results = [namedtuple("mouse_id", "mouse")(val)
for val in range(12, 20)]
results = []
-
- database_instance.execute.return_value.fetchone.side_effect = database_results
+ cursor = mock.Mock()
+ cursor.execute.return_value = 1
+ cursor.fetchone.side_effect = database_results
+ database_instance.cursor.return_value = cursor
expected_results = [12, None, 13, 14]
for (species, gene_id) in test_data:
mouse_gene_id_results = map_to_mouse_gene_id(
- database=database_instance, species=species, gene_id=gene_id)
+ conn=database_instance, species=species, gene_id=gene_id)
results.append(mouse_gene_id_results)
self.assertEqual(results, expected_results)
@@ -371,7 +385,7 @@ class TestCorrelation(TestCase):
mock_lit_corr.side_effect = expected_mocked_lit_results
lit_correlation_results = compute_all_lit_correlation(
- database_instance=database, trait_lists=[{"gene_id": 11}],
+ conn=database, trait_lists=[{"gene_id": 11}],
species="rat", gene_id=12)
expected_results = {
@@ -381,16 +395,26 @@ class TestCorrelation(TestCase):
self.assertEqual(lit_correlation_results, expected_results)
@mock.patch("gn3.computations.correlations.tissue_correlation_for_trait_list")
- def test_compute_all_tissue_correlation(self, mock_tissue_corr):
+ @mock.patch("gn3.computations.correlations.process_trait_symbol_dict")
+ def test_compute_all_tissue_correlation(self, process_trait_symbol, mock_tissue_corr):
"""Test for compute all tissue corelation which abstracts
- api calling the tissue_correlation for trait_list
- """
+ api calling the tissue_correlation for trait_list"""
primary_tissue_dict = {"trait_id": "1419792_at",
"tissue_values": [1, 2, 3, 4, 5]}
- target_tissue_dict = [{"trait_id": "1418702_a_at", "tissue_values": [1, 2, 3]},
- {"trait_id": "1412_at", "tissue_values": [1, 2, 3]}]
+ target_tissue_dict = [{"trait_id": "1418702_a_at",
+ "symbol": "zf", "tissue_values": [1, 2, 3]},
+ {"trait_id": "1412_at",
+ "symbol": "prkce", "tissue_values": [1, 2, 3]}]
+
+ process_trait_symbol.return_value = target_tissue_dict
+
+ target_trait_symbol = {"1418702_a_at": "Zf", "1412_at": "Prkce"}
+ target_symbol_tissue_vals = {"zf": [1, 2, 3], "prkce": [1, 2, 3]}
+
+ target_tissue_data = {"trait_symbol_dict": target_trait_symbol,
+ "symbol_tissue_vals_dict": target_symbol_tissue_vals}
mock_tissue_corr.side_effect = [{"tissue_corr": -0.5, "p_value": 0.9, "tissue_number": 3},
{"tissue_corr": 1.11, "p_value": 0.2, "tissue_number": 3}]
@@ -402,9 +426,49 @@ class TestCorrelation(TestCase):
results = compute_all_tissue_correlation(
primary_tissue_dict=primary_tissue_dict,
- target_tissues_dict_list=target_tissue_dict,
+ target_tissues_data=target_tissue_data,
corr_method="pearson")
+ process_trait_symbol.assert_called_once_with(
+ target_trait_symbol, target_symbol_tissue_vals)
self.assertEqual(mock_tissue_corr.call_count, 2)
self.assertEqual(results, expected_results)
+
+ def test_map_shared_keys_to_values(self):
+ """test helper function needed to integrate with genenenetwork2\
+ given a a samplelist containing dataset sampelist keys\
+ map that to given sample values """
+
+ dataset_sample_keys = ["BXD1", "BXD2", "BXD5"]
+
+ target_dataset_data = {"HCMA:_AT": [4.1, 5.6, 3.2],
+ "TXD_AT": [6.2, 5.7, 3.6, ]}
+
+ expected_results = [{"trait_id": "HCMA:_AT",
+ "trait_sample_data": {"BXD1": 4.1, "BXD2": 5.6, "BXD5": 3.2}},
+ {"trait_id": "TXD_AT",
+ "trait_sample_data": {"BXD1": 6.2, "BXD2": 5.7, "BXD5": 3.6}}]
+
+ results = map_shared_keys_to_values(
+ dataset_sample_keys, target_dataset_data)
+
+ self.assertEqual(results, expected_results)
+
+ def test_process_trait_symbol_dict(self):
+ """test for processing trait symbol dict\
+ and fetch tissue values from tissue value dict\
+ """
+ trait_symbol_dict = {"1452864_at": "Igsf10"}
+ tissue_values_dict = {"igsf10": [8.9615, 10.6375, 9.2795, 8.6605]}
+
+ expected_results = {
+ "trait_id": "1452864_at",
+ "symbol": "igsf10",
+ "tissue_values": [8.9615, 10.6375, 9.2795, 8.6605]
+ }
+
+ results = process_trait_symbol_dict(
+ trait_symbol_dict, tissue_values_dict)
+
+ self.assertEqual(results, [expected_results])