From 6d2d648126b112ca1455c6e1f2d344a4d8d27c1d Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Mon, 2 Nov 2020 11:06:36 +0300
Subject: add tests for show trait module
---
.../tests/wqflask/show_trait/test_show_trait.py | 267 +++++++++++++++++++++
1 file changed, 267 insertions(+)
create mode 100644 wqflask/tests/wqflask/show_trait/test_show_trait.py
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
new file mode 100644
index 00000000..37eae06e
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -0,0 +1,267 @@
+"""test for wqflask/show_trait/test_show_trait.py"""
+
+
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.show_trait.show_trait import check_if_attr_exists
+from wqflask.show_trait.show_trait import requests
+
+from wqflask.show_trait.show_trait import get_ncbi_summary
+
+from wqflask.show_trait.show_trait import has_num_cases
+
+from wqflask.show_trait.show_trait import get_table_widths
+
+from wqflask.show_trait.show_trait import get_categorical_variables
+from wqflask.show_trait.show_trait import get_trait_units
+
+from wqflask.show_trait.show_trait import get_nearest_marker
+
+from wqflask.show_trait.show_trait import get_genotype_scales
+
+class TraitObject:
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
+
+
+class TestTraits(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ def test_check_if_attr_exists_truthy(self):
+ """"test if attributes exists with true return"""
+ trait_obj = TraitObject({"id_type": "id"})
+ trait_obj2 = TraitObject({"sample_name": ['samp1']})
+ results = check_if_attr_exists(trait_obj, "id_type")
+ result2 = check_if_attr_exists(trait_obj2, "sample_name")
+ self.assertIsInstance(trait_obj, TraitObject)
+ self.assertEqual(results, True)
+ self.assertEqual(result2, True)
+
+ def test_check_if_attr_exists_empty_attr(self):
+ """test if attributes exists with empty attributes"""
+ trait_obj = TraitObject({"sample": ""})
+ trait_obj2 = TraitObject({"group": None})
+ result = check_if_attr_exists(trait_obj, "sample")
+ result2 = check_if_attr_exists(trait_obj, "group")
+ self.assertEqual(result, False)
+ self.assertEqual(result2, False)
+
+ def test_check_if_attr_exists_falsey(self):
+ """check if attribute exists with empty attributes"""
+ trait_obj = TraitObject({})
+ results = check_if_attr_exists(trait_obj, "any")
+ self.assertEqual(results, False)
+
+ @mock.patch("wqflask.show_trait.show_trait.requests.get")
+ @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+ def test_get_ncbi_summary_request_success(self, mock_exists, mock_get):
+ """test for getting ncbi summary with
+ successful request"""
+ trait = TraitObject({"geneid": "id"})
+ mock_exists.return_value = True
+ content_json_string = """{
+ "result":{
+ "id":{
+ "summary":"this is a summary of the geneid"
+ }
+ }
+ }
+ """
+
+ get_return_obj = TraitObject({"content": content_json_string})
+
+ mock_get.return_value = get_return_obj
+
+ results = get_ncbi_summary(trait)
+ mock_exists.assert_called_once()
+ mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
+
+ self.assertEqual(results, "this is a summary of the geneid")
+
+ @mock.patch("wqflask.show_trait.show_trait.requests.get")
+ @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+ def test_get_ncbi_summary_request_fail(self, mock_exists, mock_get_fail):
+ """test for getting ncbi summary with request fail"""
+ trait = TraitObject({"geneid": "id"})
+ mock_exists.return_value = True
+ mock_get_fail.side_effect = Exception("an error occurred")
+ content_json_string = """{
+ "result":{
+ "id":{
+ "summary":"this is a summary of the geneid"
+ }
+ }
+ }
+ """
+
+ results = get_ncbi_summary(trait)
+ self.assertEqual(results, None)
+
+ def test_hash_num_cases_is_probeset(self):
+ """test for hash num_cases with dataset.type set to Probeset"""
+ create_dataset = TraitObject({"type": "ProbeSet"})
+ create_trait = TraitObject({"dataset": create_dataset})
+
+ self.assertEqual(has_num_cases(create_trait), False)
+
+ def test_hash_num_cases_no_probeset(self):
+ """test for hash num cases with dataset.type not Probeset"""
+ create_dataset = TraitObject({"type": "Temp"})
+
+ construct_data = {
+ "nm1": TraitObject({"num_cases": False}),
+ "nm2": TraitObject({"num_cases": True}),
+ "nm3": TraitObject({"num_cases": False})
+ }
+ construct_data2 = {
+ "nm1": TraitObject({"num_cases": False}),
+ "nm2": TraitObject({"num_cases": False}),
+ "nm3": TraitObject({"num_cases": False})
+
+
+ }
+
+ create_trait = TraitObject(
+ {"dataset": create_dataset, "data": construct_data})
+ create_trait2 = TraitObject(
+ {"dataset": create_dataset, "data": construct_data2})
+
+ results = has_num_cases(create_trait)
+
+ self.assertEqual(has_num_cases(create_trait), True)
+ self.assertEqual(has_num_cases(create_trait2), False)
+
+ def test_get_table_widths(self):
+ """test for getting table widths"""
+ sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]}
+ ), TraitObject(
+ {"se_exists": False, "attributes": ["at1", "at2"]
+ })]
+
+ results_with_numcase = get_table_widths(sample_groups, True)
+ result_no_numcase = get_table_widths(sample_groups, False)
+
+ results_one_sample = get_table_widths(
+ [TraitObject({"se_exists": True, "attributes": []})], True)
+ expected_with_numcase = (450, "750px")
+ expected_no_numcase = (450, "670px")
+ expected_one_sample = (250, "540px")
+
+ self.assertEqual(results_with_numcase, expected_with_numcase)
+ self.assertEqual(result_no_numcase, expected_no_numcase)
+ self.assertEqual(results_one_sample,
+ expected_one_sample)
+
+ def test_get_categorical_variables_no_sample_attributes(self):
+ """test for getting categorical variable names with no samples"""
+ trait = TraitObject({})
+ sample_list = TraitObject({"se_exists": True, "attributes": []})
+
+ self.assertEqual(get_categorical_variables(trait, sample_list), [])
+
+ def test_get_categorical_variables_with_sample_attributes(self):
+ pass
+
+ def test_get_trait_units(self):
+ """test for gettting trait units"""
+ trait = TraitObject(
+ {"description_fmt": "[this is a description] another test [N/A]"})
+
+ trait_no_unit_type = TraitObject({"description_fmt": ""})
+
+ results = get_trait_units(trait)
+ results_no_unit = get_trait_units(trait_no_unit_type)
+ self.assertEqual(results, "this is a descriptionN/A")
+ self.assertEqual(results_no_unit, "Value")
+
+ @mock.patch("wqflask.show_trait.show_trait.g")
+ def test_get_nearest_marker(self, mock_db):
+ """test for getting nearest marker with non-empty db"""
+
+ mock_db.db.execute.return_value.fetchall.return_value = [
+ ["Geno1", "Geno2"], ["Geno3"]]
+
+ trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+
+ group_name = TraitObject({"name": "group_name"})
+
+ this_db = TraitObject({"group": group_name})
+
+ results_with_item_db = get_nearest_marker(trait, this_db)
+
+ called_with_value = """SELECT Geno.Name
+ FROM Geno, GenoXRef, GenoFreeze
+ WHERE Geno.Chr = 'test_chr' AND
+ GenoXRef.GenoId = Geno.Id AND
+ GenoFreeze.Id = GenoXRef.GenoFreezeId AND
+ GenoFreeze.Name = 'group_nameGeno'
+ ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1"""
+
+ mock_db.db.execute.assert_called_with(called_with_value)
+
+ self.assertEqual(results_with_item_db, "Geno1")
+
+ @mock.patch("wqflask.show_trait.show_trait.g")
+ def test_get_nearest_marker_empty_db(self, mock_db):
+ """test for getting nearest marker with empty db"""
+ mock_db.db.execute.return_value.fetchall.return_value = []
+
+ trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+ group_name = TraitObject({"name": "group_name"})
+ this_db = TraitObject({"group": group_name})
+
+ results_empty_db = get_nearest_marker(trait, this_db)
+ mock_db.db.execute.assert_called_once()
+ self.assertEqual(results_empty_db, "")
+
+
+ @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+ def test_get_genotype_scales_with_genofile_is_list(self,mock_get_scales):
+ """test for getting genotype scales with genofile as list """
+ #where genofile is instance of list
+ genofiles_list = [{"filename":"file1","location":"~/data/files/f1"},{"filename":"file2","location":"~/data/files/f2"},{"filename":"file3","location":"~/data/files/f3"}]
+
+ mock_get_scales.side_effect = [[["morgan", "cM"]],[["morgan", "cM"]],[["physic", "Mb"]]]
+
+ results = get_genotype_scales(genofiles_list)
+
+ expected_results = {
+ "~/data/files/f1":[["morgan","cM"]],
+ "~/data/files/f2":[["morgan","cM"]],
+ "~/data/files/f3":[["physic","Mb"]]
+ }
+
+ multiple_calls = [mock.call('~/data/files/f1'),mock.call('~/data/files/f2'),
+ mock.call('~/data/files/f3')]
+
+
+ mock_get_scales.assert_has_calls(multiple_calls)
+ self.assertEqual(results,expected_results)
+
+
+ @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+ def test_genotype_scales_with_genofile_other(self,mock_get_scales):
+ """test for getting genotype scales with genofile as a strig"""
+ file_location = "~/another_file_location"
+ mock_get_scales.return_value = [["physic","Mb"]]
+
+ expected_results = {f"{file_location}":[["physic","Mb"]]}
+
+
+ self.assertEqual(get_genotype_scales(file_location),expected_results)
+ mock_get_scales.assert_called_once_with(file_location)
+
+
+
+
+
+
+
+
--
cgit v1.2.3
From 62996d6b521379576992172fdee99468cb0260c9 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Mon, 2 Nov 2020 13:35:59 +0300
Subject: add function docstring
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 37eae06e..1b5d2265 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -45,7 +45,7 @@ class TestTraits(unittest.TestCase):
self.assertEqual(result2, True)
def test_check_if_attr_exists_empty_attr(self):
- """test if attributes exists with empty attributes"""
+ """test if attributes exists with false return"""
trait_obj = TraitObject({"sample": ""})
trait_obj2 = TraitObject({"group": None})
result = check_if_attr_exists(trait_obj, "sample")
@@ -248,7 +248,7 @@ class TestTraits(unittest.TestCase):
@mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
def test_genotype_scales_with_genofile_other(self,mock_get_scales):
- """test for getting genotype scales with genofile as a strig"""
+ """test for getting genotype scales with genofile as a string"""
file_location = "~/another_file_location"
mock_get_scales.return_value = [["physic","Mb"]]
--
cgit v1.2.3
From 2883f17236081bc11faf4c4202393998bde0924d Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Mon, 2 Nov 2020 13:50:25 +0300
Subject: add better formatting
---
.../tests/wqflask/show_trait/test_show_trait.py | 47 +++++++++-------------
1 file changed, 20 insertions(+), 27 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 1b5d2265..408797b9 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -20,6 +20,7 @@ from wqflask.show_trait.show_trait import get_nearest_marker
from wqflask.show_trait.show_trait import get_genotype_scales
+
class TraitObject:
def __init__(self, obj):
for key, value in obj.items():
@@ -141,7 +142,7 @@ class TestTraits(unittest.TestCase):
def test_get_table_widths(self):
"""test for getting table widths"""
sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]}
- ), TraitObject(
+ ), TraitObject(
{"se_exists": False, "attributes": ["at1", "at2"]
})]
@@ -221,47 +222,39 @@ class TestTraits(unittest.TestCase):
mock_db.db.execute.assert_called_once()
self.assertEqual(results_empty_db, "")
-
@mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
- def test_get_genotype_scales_with_genofile_is_list(self,mock_get_scales):
+ def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales):
"""test for getting genotype scales with genofile as list """
- #where genofile is instance of list
- genofiles_list = [{"filename":"file1","location":"~/data/files/f1"},{"filename":"file2","location":"~/data/files/f2"},{"filename":"file3","location":"~/data/files/f3"}]
+ # where genofile is instance of list
+ genofiles_list = [{"filename": "file1", "location": "~/data/files/f1"},
+ {"filename": "file2", "location": "~/data/files/f2"},
+ {"filename": "file3", "location": "~/data/files/f3"}]
- mock_get_scales.side_effect = [[["morgan", "cM"]],[["morgan", "cM"]],[["physic", "Mb"]]]
+ mock_get_scales.side_effect = [[["morgan", "cM"]],
+ [["morgan", "cM"]],
+ [["physic", "Mb"]]]
results = get_genotype_scales(genofiles_list)
expected_results = {
- "~/data/files/f1":[["morgan","cM"]],
- "~/data/files/f2":[["morgan","cM"]],
- "~/data/files/f3":[["physic","Mb"]]
+ "~/data/files/f1": [["morgan", "cM"]],
+ "~/data/files/f2": [["morgan", "cM"]],
+ "~/data/files/f3": [["physic", "Mb"]]
}
- multiple_calls = [mock.call('~/data/files/f1'),mock.call('~/data/files/f2'),
- mock.call('~/data/files/f3')]
-
+ multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'),
+ mock.call('~/data/files/f3')]
mock_get_scales.assert_has_calls(multiple_calls)
- self.assertEqual(results,expected_results)
-
+ self.assertEqual(results, expected_results)
@mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
- def test_genotype_scales_with_genofile_other(self,mock_get_scales):
+ def test_genotype_scales_with_genofile_other(self, mock_get_scales):
"""test for getting genotype scales with genofile as a string"""
file_location = "~/another_file_location"
- mock_get_scales.return_value = [["physic","Mb"]]
+ mock_get_scales.return_value = [["physic", "Mb"]]
- expected_results = {f"{file_location}":[["physic","Mb"]]}
+ expected_results = {f"{file_location}": [["physic", "Mb"]]}
-
- self.assertEqual(get_genotype_scales(file_location),expected_results)
+ self.assertEqual(get_genotype_scales(file_location), expected_results)
mock_get_scales.assert_called_once_with(file_location)
-
-
-
-
-
-
-
-
--
cgit v1.2.3
From 251113ee34819afdc3e2abc63d59a01bd6a560cb Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Tue, 3 Nov 2020 10:32:36 +0300
Subject: use assertTrue and assertFalse in while testing boolean
---
.../tests/wqflask/show_trait/test_show_trait.py | 38 ++++++++--------------
1 file changed, 13 insertions(+), 25 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 408797b9..a2ef71dd 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -1,24 +1,12 @@
"""test for wqflask/show_trait/test_show_trait.py"""
-
import unittest
from unittest import mock
from wqflask import app
-from wqflask.show_trait.show_trait import check_if_attr_exists
-from wqflask.show_trait.show_trait import requests
-
-from wqflask.show_trait.show_trait import get_ncbi_summary
-
-from wqflask.show_trait.show_trait import has_num_cases
-
-from wqflask.show_trait.show_trait import get_table_widths
-
-from wqflask.show_trait.show_trait import get_categorical_variables
-from wqflask.show_trait.show_trait import get_trait_units
-
-from wqflask.show_trait.show_trait import get_nearest_marker
-
-from wqflask.show_trait.show_trait import get_genotype_scales
+from wqflask.show_trait.show_trait import (check_if_attr_exists, get_ncbi_summary,
+ has_num_cases, get_table_widths,
+ get_categorical_variables,
+ get_trait_units, get_nearest_marker, get_genotype_scales, requests)
class TraitObject:
@@ -42,8 +30,8 @@ class TestTraits(unittest.TestCase):
results = check_if_attr_exists(trait_obj, "id_type")
result2 = check_if_attr_exists(trait_obj2, "sample_name")
self.assertIsInstance(trait_obj, TraitObject)
- self.assertEqual(results, True)
- self.assertEqual(result2, True)
+ self.assertTrue(results, True)
+ self.assertTrue(result2, True)
def test_check_if_attr_exists_empty_attr(self):
"""test if attributes exists with false return"""
@@ -51,14 +39,14 @@ class TestTraits(unittest.TestCase):
trait_obj2 = TraitObject({"group": None})
result = check_if_attr_exists(trait_obj, "sample")
result2 = check_if_attr_exists(trait_obj, "group")
- self.assertEqual(result, False)
- self.assertEqual(result2, False)
+ self.assertFalse(result, False)
+ self.assertFalse(result2, False)
def test_check_if_attr_exists_falsey(self):
"""check if attribute exists with empty attributes"""
trait_obj = TraitObject({})
results = check_if_attr_exists(trait_obj, "any")
- self.assertEqual(results, False)
+ self.assertFalse(results, False)
@mock.patch("wqflask.show_trait.show_trait.requests.get")
@mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
@@ -110,7 +98,7 @@ class TestTraits(unittest.TestCase):
create_dataset = TraitObject({"type": "ProbeSet"})
create_trait = TraitObject({"dataset": create_dataset})
- self.assertEqual(has_num_cases(create_trait), False)
+ self.assertFalse(has_num_cases(create_trait), False)
def test_hash_num_cases_no_probeset(self):
"""test for hash num cases with dataset.type not Probeset"""
@@ -136,8 +124,8 @@ class TestTraits(unittest.TestCase):
results = has_num_cases(create_trait)
- self.assertEqual(has_num_cases(create_trait), True)
- self.assertEqual(has_num_cases(create_trait2), False)
+ self.assertTrue(has_num_cases(create_trait), True)
+ self.assertFalse(has_num_cases(create_trait2), False)
def test_get_table_widths(self):
"""test for getting table widths"""
@@ -171,7 +159,7 @@ class TestTraits(unittest.TestCase):
pass
def test_get_trait_units(self):
- """test for gettting trait units"""
+ """test for getting trait units"""
trait = TraitObject(
{"description_fmt": "[this is a description] another test [N/A]"})
--
cgit v1.2.3
From ef0c9bb30523b32decc163dcb62c125e7ba5a076 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Tue, 3 Nov 2020 16:50:23 +0300
Subject: switch from assertTrue/False to assertIs to make the tests tighter
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index a2ef71dd..f666912b 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -1,5 +1,4 @@
"""test for wqflask/show_trait/test_show_trait.py"""
-
import unittest
from unittest import mock
from wqflask import app
@@ -30,8 +29,9 @@ class TestTraits(unittest.TestCase):
results = check_if_attr_exists(trait_obj, "id_type")
result2 = check_if_attr_exists(trait_obj2, "sample_name")
self.assertIsInstance(trait_obj, TraitObject)
- self.assertTrue(results, True)
- self.assertTrue(result2, True)
+ self.assertIs(results, True)
+ self.assertIs(result2, True)
+
def test_check_if_attr_exists_empty_attr(self):
"""test if attributes exists with false return"""
@@ -39,14 +39,14 @@ class TestTraits(unittest.TestCase):
trait_obj2 = TraitObject({"group": None})
result = check_if_attr_exists(trait_obj, "sample")
result2 = check_if_attr_exists(trait_obj, "group")
- self.assertFalse(result, False)
- self.assertFalse(result2, False)
+ self.assertIs(result, False)
+ self.assertIs(result2, False)
def test_check_if_attr_exists_falsey(self):
"""check if attribute exists with empty attributes"""
trait_obj = TraitObject({})
results = check_if_attr_exists(trait_obj, "any")
- self.assertFalse(results, False)
+ self.assertIs(results, False)
@mock.patch("wqflask.show_trait.show_trait.requests.get")
@mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
@@ -124,8 +124,8 @@ class TestTraits(unittest.TestCase):
results = has_num_cases(create_trait)
- self.assertTrue(has_num_cases(create_trait), True)
- self.assertFalse(has_num_cases(create_trait2), False)
+ self.assertIs(has_num_cases(create_trait), True)
+ self.assertIs(has_num_cases(create_trait2), False)
def test_get_table_widths(self):
"""test for getting table widths"""
--
cgit v1.2.3
From 7da9a5206800d305f97b025e180300ca451ac92d Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Tue, 3 Nov 2020 17:08:05 +0300
Subject: switch from assertFalse to assertIs
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index f666912b..ec45d558 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -31,7 +31,6 @@ class TestTraits(unittest.TestCase):
self.assertIsInstance(trait_obj, TraitObject)
self.assertIs(results, True)
self.assertIs(result2, True)
-
def test_check_if_attr_exists_empty_attr(self):
"""test if attributes exists with false return"""
@@ -98,7 +97,7 @@ class TestTraits(unittest.TestCase):
create_dataset = TraitObject({"type": "ProbeSet"})
create_trait = TraitObject({"dataset": create_dataset})
- self.assertFalse(has_num_cases(create_trait), False)
+ self.assertIs(has_num_cases(create_trait), False)
def test_hash_num_cases_no_probeset(self):
"""test for hash num cases with dataset.type not Probeset"""
--
cgit v1.2.3
From 4b6d964ccf484225f568361b3bc6136a758cd475 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Tue, 3 Nov 2020 20:15:39 +0300
Subject: add tests for the get_categorical_variables function
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index ec45d558..f7133292 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -155,7 +155,22 @@ class TestTraits(unittest.TestCase):
self.assertEqual(get_categorical_variables(trait, sample_list), [])
def test_get_categorical_variables_with_sample_attributes(self):
- pass
+ this_trait=TraitObject({"data":{
+ "Gene1":TraitObject({"extra_attributes":{"ex1":"ex1value"}}),
+ "Gene2":TraitObject({"extra_attributes":{"ex2":"ex2value"}}),
+ "Gene3":TraitObject({"extra_attributes":{"ex3":"ex3value"}})
+ }})
+ sample_list=TraitObject({"attributes":{
+ "sample_attribute_1":TraitObject({"name":"ex1"}),
+ "sample_attribute_2":TraitObject({"name":"ex2"}),
+ "sample_attribute_3":TraitObject({"name":"ex3"}),
+ "sample_attribute_4":TraitObject({"name":"not_in_extra_attributes"}),
+
+
+ }})
+
+ results=get_categorical_variables(this_trait,sample_list)
+ self.assertEqual(["ex1","ex2","ex3","not_in_extra_attributes"],results)
def test_get_trait_units(self):
"""test for getting trait units"""
--
cgit v1.2.3
From 68f71e11343789266ccac6e079dd0bc1b16d407f Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Tue, 3 Nov 2020 20:23:19 +0300
Subject: add pep8 formatting
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index f7133292..f41b7288 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -155,6 +155,7 @@ class TestTraits(unittest.TestCase):
self.assertEqual(get_categorical_variables(trait, sample_list), [])
def test_get_categorical_variables_with_sample_attributes(self):
+ """test for getting categorical variable names with no samples"""
this_trait=TraitObject({"data":{
"Gene1":TraitObject({"extra_attributes":{"ex1":"ex1value"}}),
"Gene2":TraitObject({"extra_attributes":{"ex2":"ex2value"}}),
@@ -169,6 +170,8 @@ class TestTraits(unittest.TestCase):
}})
+ #
+
results=get_categorical_variables(this_trait,sample_list)
self.assertEqual(["ex1","ex2","ex3","not_in_extra_attributes"],results)
--
cgit v1.2.3
From 8630b727d80f52b3e846c9eb3bf7dd4e844fa626 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Tue, 3 Nov 2020 20:34:00 +0300
Subject: remove unnecessary comments
---
.../tests/wqflask/show_trait/test_show_trait.py | 35 +++++++++++-----------
1 file changed, 17 insertions(+), 18 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index f41b7288..c617e9f2 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -156,24 +156,23 @@ class TestTraits(unittest.TestCase):
def test_get_categorical_variables_with_sample_attributes(self):
"""test for getting categorical variable names with no samples"""
- this_trait=TraitObject({"data":{
- "Gene1":TraitObject({"extra_attributes":{"ex1":"ex1value"}}),
- "Gene2":TraitObject({"extra_attributes":{"ex2":"ex2value"}}),
- "Gene3":TraitObject({"extra_attributes":{"ex3":"ex3value"}})
- }})
- sample_list=TraitObject({"attributes":{
- "sample_attribute_1":TraitObject({"name":"ex1"}),
- "sample_attribute_2":TraitObject({"name":"ex2"}),
- "sample_attribute_3":TraitObject({"name":"ex3"}),
- "sample_attribute_4":TraitObject({"name":"not_in_extra_attributes"}),
-
-
- }})
-
- #
-
- results=get_categorical_variables(this_trait,sample_list)
- self.assertEqual(["ex1","ex2","ex3","not_in_extra_attributes"],results)
+ this_trait = TraitObject({"data": {
+ "Gene1": TraitObject({"extra_attributes": {"ex1": "ex1value"}}),
+ "Gene2": TraitObject({"extra_attributes": {"ex2": "ex2value"}}),
+ "Gene3": TraitObject({"extra_attributes": {"ex3": "ex3value"}})
+ }})
+ sample_list = TraitObject({"attributes": {
+ "sample_attribute_1": TraitObject({"name": "ex1"}),
+ "sample_attribute_2": TraitObject({"name": "ex2"}),
+ "sample_attribute_3": TraitObject({"name": "ex3"}),
+ "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"}),
+
+
+ }})
+
+ results = get_categorical_variables(this_trait, sample_list)
+ self.assertEqual(
+ ["ex1", "ex2", "ex3", "not_in_extra_attributes"], results)
def test_get_trait_units(self):
"""test for getting trait units"""
--
cgit v1.2.3
From 23915d8102b8a05930cf3fd16d651a460ebd2f58 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Wed, 4 Nov 2020 09:49:13 +0300
Subject: remove whitespace and assertIs
---
.../tests/wqflask/show_trait/test_show_trait.py | 30 ++++++++++++----------
1 file changed, 17 insertions(+), 13 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index c617e9f2..04c68045 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -2,11 +2,15 @@
import unittest
from unittest import mock
from wqflask import app
-from wqflask.show_trait.show_trait import (check_if_attr_exists, get_ncbi_summary,
- has_num_cases, get_table_widths,
- get_categorical_variables,
- get_trait_units, get_nearest_marker, get_genotype_scales, requests)
-
+from wqflask.show_trait.show_trait import check_if_attr_exists
+from wqflask.show_trait.show_trait import get_ncbi_summary
+from wqflask.show_trait.show_trait import has_num_cases
+from wqflask.show_trait.show_trait import get_table_widths
+from wqflask.show_trait.show_trait import get_categorical_variables
+from wqflask.show_trait.show_trait import get_trait_units
+from wqflask.show_trait.show_trait import get_nearest_marker
+from wqflask.show_trait.show_trait import get_genotype_scales
+from wqflask.show_trait.show_trait import requests
class TraitObject:
def __init__(self, obj):
@@ -29,8 +33,8 @@ class TestTraits(unittest.TestCase):
results = check_if_attr_exists(trait_obj, "id_type")
result2 = check_if_attr_exists(trait_obj2, "sample_name")
self.assertIsInstance(trait_obj, TraitObject)
- self.assertIs(results, True)
- self.assertIs(result2, True)
+ self.assertTrue(results)
+ self.assertTrue(result2)
def test_check_if_attr_exists_empty_attr(self):
"""test if attributes exists with false return"""
@@ -38,14 +42,14 @@ class TestTraits(unittest.TestCase):
trait_obj2 = TraitObject({"group": None})
result = check_if_attr_exists(trait_obj, "sample")
result2 = check_if_attr_exists(trait_obj, "group")
- self.assertIs(result, False)
- self.assertIs(result2, False)
+ self.assertFalse(result)
+ self.assertFalse(result2)
def test_check_if_attr_exists_falsey(self):
"""check if attribute exists with empty attributes"""
trait_obj = TraitObject({})
results = check_if_attr_exists(trait_obj, "any")
- self.assertIs(results, False)
+ self.assertFalse(results)
@mock.patch("wqflask.show_trait.show_trait.requests.get")
@mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
@@ -97,7 +101,7 @@ class TestTraits(unittest.TestCase):
create_dataset = TraitObject({"type": "ProbeSet"})
create_trait = TraitObject({"dataset": create_dataset})
- self.assertIs(has_num_cases(create_trait), False)
+ self.assertFalse(has_num_cases(create_trait))
def test_hash_num_cases_no_probeset(self):
"""test for hash num cases with dataset.type not Probeset"""
@@ -123,8 +127,8 @@ class TestTraits(unittest.TestCase):
results = has_num_cases(create_trait)
- self.assertIs(has_num_cases(create_trait), True)
- self.assertIs(has_num_cases(create_trait2), False)
+ self.assertTrue(has_num_cases(create_trait))
+ self.assertFalse(has_num_cases(create_trait2))
def test_get_table_widths(self):
"""test for getting table widths"""
--
cgit v1.2.3
From 9d2134202c0435ad4a18e0ac74ce4a99508f1a76 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Wed, 4 Nov 2020 09:57:35 +0300
Subject: remove whitespace
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 04c68045..f82a4c04 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -3,7 +3,7 @@ import unittest
from unittest import mock
from wqflask import app
from wqflask.show_trait.show_trait import check_if_attr_exists
-from wqflask.show_trait.show_trait import get_ncbi_summary
+from wqflask.show_trait.show_trait import get_ncbi_summary
from wqflask.show_trait.show_trait import has_num_cases
from wqflask.show_trait.show_trait import get_table_widths
from wqflask.show_trait.show_trait import get_categorical_variables
@@ -12,6 +12,7 @@ from wqflask.show_trait.show_trait import get_nearest_marker
from wqflask.show_trait.show_trait import get_genotype_scales
from wqflask.show_trait.show_trait import requests
+
class TraitObject:
def __init__(self, obj):
for key, value in obj.items():
@@ -169,9 +170,7 @@ class TestTraits(unittest.TestCase):
"sample_attribute_1": TraitObject({"name": "ex1"}),
"sample_attribute_2": TraitObject({"name": "ex2"}),
"sample_attribute_3": TraitObject({"name": "ex3"}),
- "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"}),
-
-
+ "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"})
}})
results = get_categorical_variables(this_trait, sample_list)
--
cgit v1.2.3
From 1ef7c3cd7bc148bac8a6b47f62ba02c3819bf1f3 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Wed, 4 Nov 2020 10:08:32 +0300
Subject: remove whitespace in line 119-120
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 2 --
1 file changed, 2 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index f82a4c04..70061e2d 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -117,8 +117,6 @@ class TestTraits(unittest.TestCase):
"nm1": TraitObject({"num_cases": False}),
"nm2": TraitObject({"num_cases": False}),
"nm3": TraitObject({"num_cases": False})
-
-
}
create_trait = TraitObject(
--
cgit v1.2.3
From f90e77fab78c4504ac9dabb188459ab5d03ac287 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Wed, 4 Nov 2020 10:15:05 +0300
Subject: remove extra whitespace
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 21 ---------------------
1 file changed, 21 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 70061e2d..ce850c8b 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -67,11 +67,8 @@ class TestTraits(unittest.TestCase):
}
}
"""
-
get_return_obj = TraitObject({"content": content_json_string})
-
mock_get.return_value = get_return_obj
-
results = get_ncbi_summary(trait)
mock_exists.assert_called_once()
mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
@@ -93,7 +90,6 @@ class TestTraits(unittest.TestCase):
}
}
"""
-
results = get_ncbi_summary(trait)
self.assertEqual(results, None)
@@ -101,13 +97,11 @@ class TestTraits(unittest.TestCase):
"""test for hash num_cases with dataset.type set to Probeset"""
create_dataset = TraitObject({"type": "ProbeSet"})
create_trait = TraitObject({"dataset": create_dataset})
-
self.assertFalse(has_num_cases(create_trait))
def test_hash_num_cases_no_probeset(self):
"""test for hash num cases with dataset.type not Probeset"""
create_dataset = TraitObject({"type": "Temp"})
-
construct_data = {
"nm1": TraitObject({"num_cases": False}),
"nm2": TraitObject({"num_cases": True}),
@@ -125,7 +119,6 @@ class TestTraits(unittest.TestCase):
{"dataset": create_dataset, "data": construct_data2})
results = has_num_cases(create_trait)
-
self.assertTrue(has_num_cases(create_trait))
self.assertFalse(has_num_cases(create_trait2))
@@ -144,7 +137,6 @@ class TestTraits(unittest.TestCase):
expected_with_numcase = (450, "750px")
expected_no_numcase = (450, "670px")
expected_one_sample = (250, "540px")
-
self.assertEqual(results_with_numcase, expected_with_numcase)
self.assertEqual(result_no_numcase, expected_no_numcase)
self.assertEqual(results_one_sample,
@@ -154,7 +146,6 @@ class TestTraits(unittest.TestCase):
"""test for getting categorical variable names with no samples"""
trait = TraitObject({})
sample_list = TraitObject({"se_exists": True, "attributes": []})
-
self.assertEqual(get_categorical_variables(trait, sample_list), [])
def test_get_categorical_variables_with_sample_attributes(self):
@@ -179,9 +170,7 @@ class TestTraits(unittest.TestCase):
"""test for getting trait units"""
trait = TraitObject(
{"description_fmt": "[this is a description] another test [N/A]"})
-
trait_no_unit_type = TraitObject({"description_fmt": ""})
-
results = get_trait_units(trait)
results_no_unit = get_trait_units(trait_no_unit_type)
self.assertEqual(results, "this is a descriptionN/A")
@@ -195,13 +184,9 @@ class TestTraits(unittest.TestCase):
["Geno1", "Geno2"], ["Geno3"]]
trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
-
group_name = TraitObject({"name": "group_name"})
-
this_db = TraitObject({"group": group_name})
-
results_with_item_db = get_nearest_marker(trait, this_db)
-
called_with_value = """SELECT Geno.Name
FROM Geno, GenoXRef, GenoFreeze
WHERE Geno.Chr = 'test_chr' AND
@@ -218,11 +203,9 @@ class TestTraits(unittest.TestCase):
def test_get_nearest_marker_empty_db(self, mock_db):
"""test for getting nearest marker with empty db"""
mock_db.db.execute.return_value.fetchall.return_value = []
-
trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
group_name = TraitObject({"name": "group_name"})
this_db = TraitObject({"group": group_name})
-
results_empty_db = get_nearest_marker(trait, this_db)
mock_db.db.execute.assert_called_once()
self.assertEqual(results_empty_db, "")
@@ -240,7 +223,6 @@ class TestTraits(unittest.TestCase):
[["physic", "Mb"]]]
results = get_genotype_scales(genofiles_list)
-
expected_results = {
"~/data/files/f1": [["morgan", "cM"]],
"~/data/files/f2": [["morgan", "cM"]],
@@ -249,7 +231,6 @@ class TestTraits(unittest.TestCase):
multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'),
mock.call('~/data/files/f3')]
-
mock_get_scales.assert_has_calls(multiple_calls)
self.assertEqual(results, expected_results)
@@ -258,8 +239,6 @@ class TestTraits(unittest.TestCase):
"""test for getting genotype scales with genofile as a string"""
file_location = "~/another_file_location"
mock_get_scales.return_value = [["physic", "Mb"]]
-
expected_results = {f"{file_location}": [["physic", "Mb"]]}
-
self.assertEqual(get_genotype_scales(file_location), expected_results)
mock_get_scales.assert_called_once_with(file_location)
--
cgit v1.2.3
From 3f08f54fe3d42eca0ccf98831e4e339defa17720 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Wed, 4 Nov 2020 10:25:50 +0300
Subject: correct a typo
---
wqflask/tests/wqflask/show_trait/test_show_trait.py | 2 --
1 file changed, 2 deletions(-)
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index ce850c8b..24150738 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -112,7 +112,6 @@ class TestTraits(unittest.TestCase):
"nm2": TraitObject({"num_cases": False}),
"nm3": TraitObject({"num_cases": False})
}
-
create_trait = TraitObject(
{"dataset": create_dataset, "data": construct_data})
create_trait2 = TraitObject(
@@ -161,7 +160,6 @@ class TestTraits(unittest.TestCase):
"sample_attribute_3": TraitObject({"name": "ex3"}),
"sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"})
}})
-
results = get_categorical_variables(this_trait, sample_list)
self.assertEqual(
["ex1", "ex2", "ex3", "not_in_extra_attributes"], results)
--
cgit v1.2.3