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-rw-r--r--tests/unit/computations/test_correlation.py73
-rw-r--r--tests/unit/computations/test_datasets.py55
-rw-r--r--tests/unit/computations/test_trait.py16
3 files changed, 82 insertions, 62 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 84b9330..631dc18 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -1,4 +1,4 @@
-"""module contains the tests for correlation"""
+"""Module contains the tests for correlation"""
import unittest
from unittest import TestCase
from unittest import mock
@@ -80,10 +80,10 @@ class DataBase(QueryableMixin):
class TestCorrelation(TestCase):
- """class for testing correlation functions"""
+ """Class for testing correlation functions"""
def test_normalize_values(self):
- """function to test normalizing values """
+ """Function to test normalizing values """
results = normalize_values([2.3, None, None, 3.2, 4.1, 5],
[3.4, 7.2, 1.3, None, 6.2, 4.1])
@@ -92,7 +92,7 @@ class TestCorrelation(TestCase):
self.assertEqual(results, expected_results)
def test_bicor(self):
- """test for doing biweight mid correlation """
+ """Test for doing biweight mid correlation """
results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6])
@@ -102,8 +102,9 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
@mock.patch("gn3.computations.correlations.normalize_values")
def test_compute_sample_r_correlation(self, norm_vals, compute_corr):
- """test for doing sample correlation gets the cor\
- and p value and rho value using pearson correlation"""
+ """Test for doing sample correlation gets the cor\
+ and p value and rho value using pearson correlation
+ """
primary_values = [2.3, 4.1, 5]
target_values = [3.4, 6.2, 4.1]
@@ -133,7 +134,7 @@ class TestCorrelation(TestCase):
spearman_results, tuple, "message")
def test_filter_shared_sample_keys(self):
- """function to tests shared key between two dicts"""
+ """Function to tests shared key between two dicts"""
this_samplelist = {
"C57BL/6J": "6.638",
@@ -162,7 +163,7 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.compute_sample_r_correlation")
@mock.patch("gn3.computations.correlations.filter_shared_sample_keys")
def test_compute_all_sample(self, filter_shared_samples, sample_r_corr):
- """given target dataset compute all sample r correlation"""
+ """Given target dataset compute all sample r correlation"""
filter_shared_samples.return_value = (["1.23", "6.565", "6.456"], [
"6.266", "6.565", "6.456"])
@@ -192,7 +193,6 @@ class TestCorrelation(TestCase):
sample_all_results = [{"1419792_at": {"corr_coeffient": -1.0,
"p_value": 0.9,
"num_overlap": 6}}]
- # ?corr_method: str, trait_vals, target_samples_vals
self.assertEqual(compute_all_sample_correlation(
this_trait=this_trait_data, target_dataset=traits_dataset), sample_all_results)
@@ -204,9 +204,10 @@ class TestCorrelation(TestCase):
@unittest.skip("not implemented")
def test_tissue_lit_corr_for_probe_type(self):
- """tests for doing tissue and lit correlation for trait list\
+ """Tests for doing tissue and lit correlation for trait list\
if both the dataset and target dataset are probeset runs\
- on after initial correlation has been done"""
+ on after initial correlation has been done
+ """
results = tissue_lit_corr_for_probe_type(
corr_type="tissue", top_corr_results={})
@@ -215,8 +216,9 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
def test_tissue_correlation_for_trait_list(self, mock_compute_corr_coeff):
- """test given a primary tissue values for a trait and and a list of\
- target tissues for traits do the tissue correlation for them"""
+ """Test given a primary tissue values for a trait and and a list of\
+ target tissues for traits do the tissue correlation for them
+ """
primary_tissue_values = [1.1, 1.5, 2.3]
target_tissues_values = [1, 2, 3]
@@ -233,8 +235,9 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.fetch_lit_correlation_data")
@mock.patch("gn3.computations.correlations.map_to_mouse_gene_id")
def test_lit_correlation_for_trait_list(self, mock_mouse_gene_id, fetch_lit_data):
- """fetch results from db call for lit correlation given a trait list\
- after doing correlation"""
+ """Fetch results from db call for lit correlation given a trait list\
+ after doing correlation
+ """
target_trait_lists = [{"gene_id": 15},
{"gene_id": 17},
@@ -255,8 +258,9 @@ class TestCorrelation(TestCase):
self.assertEqual(lit_results, expected_results)
def test_fetch_lit_correlation_data(self):
- """test for fetching lit correlation data from\
- the database where the input and mouse geneid are none"""
+ """Test for fetching lit correlation data from\
+ the database where the input and mouse geneid are none
+ """
database_instance = DataBase()
results = fetch_lit_correlation_data(database=database_instance,
@@ -267,8 +271,9 @@ class TestCorrelation(TestCase):
self.assertEqual(results, ("1", 0))
def test_fetch_lit_correlation_data_db_query(self):
- """test for fetching lit corr coefficent givent the input\
- input trait mouse gene id and mouse gene id"""
+ """Test for fetching lit corr coefficent givent the input\
+ input trait mouse gene id and mouse gene id
+ """
database_instance = DataBase()
expected_results = ("1", 0.1)
@@ -281,8 +286,9 @@ class TestCorrelation(TestCase):
self.assertEqual(expected_results, lit_results)
def test_query_lit_correlation_for_db_empty(self):
- """test that corr coeffient returned is 0 given the\
- db value if corr coefficient is empty"""
+ """Test that corr coeffient returned is 0 given the\
+ db value if corr coefficient is empty
+ """
database_instance = mock.Mock()
database_instance.execute.return_value.fetchone.return_value = None
@@ -294,8 +300,9 @@ class TestCorrelation(TestCase):
self.assertEqual(lit_results, ("16", 0))
def test_query_formatter(self):
- """test for formatting a query given the query string and also the\
- values"""
+ """Test for formatting a query given the query string and also the\
+ values
+ """
query = """
SELECT VALUE
FROM LCorr
@@ -320,16 +327,18 @@ class TestCorrelation(TestCase):
self.assertEqual(formatted_query, expected_formatted_query)
def test_query_formatter_no_query_values(self):
- """test for formatting a query where there are no\
- string placeholder"""
+ """Test for formatting a query where there are no\
+ string placeholder
+ """
query = """SELECT * FROM USERS"""
formatted_query = query_formatter(query)
self.assertEqual(formatted_query, query)
def test_map_to_mouse_gene_id(self):
- """test for converting a gene id to mouse geneid\
- given a species which is not mouse"""
+ """Test for converting a gene id to mouse geneid\
+ given a species which is not mouse
+ """
database_instance = mock.Mock()
test_data = [("Human", 14), (None, 9), ("Mouse", 15), ("Rat", 14)]
@@ -349,9 +358,10 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.lit_correlation_for_trait_list")
def test_compute_all_lit_correlation(self, mock_lit_corr):
- """test for compute all lit correlation which acts\
+ """Test for compute all lit correlation which acts\
as an abstraction for lit_correlation_for_trait_list
- and is used in the api/correlation/lit"""
+ and is used in the api/correlation/lit
+ """
database = mock.Mock()
@@ -372,8 +382,9 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.tissue_correlation_for_trait_list")
def test_compute_all_tissue_correlation(self, mock_tissue_corr):
- """test for compute all tissue corelation which abstracts
- api calling the tissue_correlation for trait_list"""
+ """Test for compute all tissue corelation which abstracts
+ api calling the tissue_correlation for trait_list
+ """
primary_tissue_dict = {"trait_id": "1419792_at",
"tissue_values": [1, 2, 3, 4, 5]}
diff --git a/tests/unit/computations/test_datasets.py b/tests/unit/computations/test_datasets.py
index 44ff527..f9e9c2b 100644
--- a/tests/unit/computations/test_datasets.py
+++ b/tests/unit/computations/test_datasets.py
@@ -1,4 +1,4 @@
-"""module contains tests from datasets"""
+"""Module contains tests from datasets"""
import json
from unittest import TestCase
@@ -19,12 +19,13 @@ from gn3.computations.datasets import get_traits_data
class TestDatasets(TestCase):
- """class contains tests for datasets"""
+ """Class contains tests for datasets"""
@mock.patch("gn3.computations.datasets.fetch_from_db_sample_data")
def test_retrieve_trait_sample_data(self, mock_fetch_sample_results):
- """test retrieving sample data\
- for trait from the dataset"""
+ """Test retrieving sample data\
+ for trait from the dataset
+ """
trait_name = "1419792_at"
dataset_id = "HC_M2_0606_P&"
dataset_type = "Publish"
@@ -47,7 +48,7 @@ class TestDatasets(TestCase):
self.assertEqual(results, fetch_results)
def test_query_for_dataset_sample(self):
- """test for getting query for sample data"""
+ """Test for getting query for sample data"""
no_results = get_query_for_dataset_sample("does not exists")
@@ -57,8 +58,9 @@ class TestDatasets(TestCase):
self.assertIsInstance(query_exists, str)
def test_fetch_from_db_sample_data(self):
- """test for function that fetches sample\
- results from the database"""
+ """Test for function that fetches sample\
+ results from the database
+ """
database_results = [('BXD31', 8.001, None, None, 'BXD31'),
('BXD32', 7.884, None, None, 'BXD32'),
@@ -91,9 +93,10 @@ class TestDatasets(TestCase):
@mock.patch("gn3.computations.datasets.dataset_creator_store")
@mock.patch("gn3.computations.datasets.dataset_type_getter")
def test_create_dataset(self, mock_dataset_type, mock_store):
- """test function that creates/fetches required dataset\
+ """Test function that creates/fetches required dataset\
can either be published phenotype,genotype,Microarray or\
- user defined ->Temp"""
+ user defined ->Temp
+ """
probe_name = "HC_M2_0606_P"
probe_type = "ProbeSet"
@@ -109,28 +112,31 @@ class TestDatasets(TestCase):
self.assertEqual(dataset.dataset_type, probe_type)
def test_dataset_creator_store(self):
- """test for functions that actual
+ """Test for functions that actual
function to create differerent \
- datasets"""
+ datasets
+ """
results = dataset_creator_store("ProbeSet")
self.assertTrue(results)
def test_dataset_type_getter(self):
- """test for fetching type of dataset given\
- the dataset name"""
+ """Test for fetching type of dataset given\
+ the dataset name
+ """
redis_instance = mock.Mock()
- # found in redis
+ # fetched in redis
redis_instance.get.return_value = "ProbeSet"
results = dataset_type_getter("HC_M2_0_P", redis_instance)
self.assertEqual(results, "ProbeSet")
@mock.patch("gn3.computations.datasets.requests")
def test_fetch_dataset_type_from_gn2_api(self, mock_request):
- """test for function that test fetching\
+ """Test for function that test fetching\
all datasets from gn2 api in order to store\
- in redis"""
+ in redis
+ """
expected_json_results = {"datasets": {
"arabidopsis": {
@@ -164,8 +170,9 @@ class TestDatasets(TestCase):
self.assertEqual(expected_results, results)
def test_fetch_dataset_sample_id(self):
- """get from the database the sample\
- id if only in the samplelists"""
+ """Get from the database the sample\
+ id if only in the samplelists
+ """
expected_results = {"B6D2F1": 1, "BXD1": 4, "BXD11": 10,
"BXD12": 11, "BXD13": 12, "BXD15": 14, "BXD16": 15}
@@ -187,10 +194,9 @@ class TestDatasets(TestCase):
@mock.patch("gn3.computations.datasets.fetch_from_db_sample_data")
@mock.patch("gn3.computations.datasets.divide_into_chunks")
def test_get_traits_data(self, mock_divide_into_chunks, mock_fetch_samples):
- """test for for function to get data\
- of traits in dataset"""
- # xtodo more tests needed for this
-
+ """Test for for function to get data\
+ of traits in dataset
+ """
_expected_results = {'AT_DSAFDS': [
12, 14, 13, 23, 12, 14, 13, 23, 12, 14, 13, 23]}
database = mock.Mock()
@@ -203,8 +209,9 @@ class TestDatasets(TestCase):
self.assertEqual({}, dict(results))
def test_divide_into_chunks(self):
- """test for dividing a list into given number of\
- chunks for example"""
+ """Test for dividing a list into given number of\
+ chunks for example
+ """
results = divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3)
expected_results = [[1, 2, 7], [3, 22, 8], [5, 22, 333]]
diff --git a/tests/unit/computations/test_trait.py b/tests/unit/computations/test_trait.py
index cdd8078..feb97c6 100644
--- a/tests/unit/computations/test_trait.py
+++ b/tests/unit/computations/test_trait.py
@@ -1,4 +1,4 @@
-"""module contains tests for creating traits"""
+"""Module contains tests for creating traits"""
from unittest import TestCase
from unittest import mock
@@ -8,11 +8,11 @@ from gn3.computations.traits import get_trait_info_data
class TestTrait(TestCase):
- """class contains tests for creating traits"""
+ """Class contains tests for creating traits"""
@mock.patch("gn3.computations.traits.get_trait_sample_data")
def test_fetch_trait(self, get_sample_data):
- """test for creating/fetching trait"""
+ """Test for creating/fetching trait"""
expected_sample_data = {
"A/Y": 12.3,
@@ -37,8 +37,9 @@ class TestTrait(TestCase):
@mock.patch("gn3.computations.traits.retrieve_trait_sample_data")
def test_get_trait_sample_data(self, mock_retrieve_sample_data):
- """test for getting sample data from either\
- the trait's dataset or form redis"""
+ """Test for getting sample data from either\
+ the trait's dataset or form redis
+ """
trait_dataset = mock.Mock()
dataset_trait_sample_data = [
@@ -65,8 +66,9 @@ class TestTrait(TestCase):
self.assertEqual(results, expected_results)
def test_get_trait_info_data(self):
- """test for getting info data related\
- to trait"""
+ """Test for getting info data related\
+ to trait
+ """
results = get_trait_info_data(
trait_name="AXSF_AT", trait_dataset=mock.Mock(), database_instance=None)