small helpers

Clinical-Genomics · Sep 30, 2020 · 7d86ffb · 7d86ffb
1 parent b149ca5
commit 7d86ffb
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diff --git a/tests/__init__.py b/tests/__init__.py
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,6 +1,8 @@
 import pytest
 
 from mongomock import MongoClient
+from .small_helpers import SmallHelpers
+
 
 DATABASE = "testdb"
 
@@ -27,114 +29,10 @@ def database(request, pymongo_client):
     return database
 
 
-def batch(
-    batch_id = "201860",
-    sequencing_date = "2022-03-10",
-    stdev_13= 0.0095,
-    stdev_18 = 0.0035,
-    stdev_21 = 0.0085,
-):
-    """A batch mock"""
-
-    return {
-        "_id": batch_id,
-        "SequencingDate": sequencing_date,
-        "Median_13": 0.994623404680424,
-        "Median_18": 1.01950547134618,
-        "Median_21": 1.00710552415657,
-        "Median_X": 0.8408228472301729,
-        "Median_Y": 0.00011224982090899999,
-        "Stdev_13": stdev_13,
-        "Stdev_18": stdev_18,
-        "Stdev_21": stdev_21,
-        "Stdev_X": 0.029800076293786,
-        "Stdev_Y": 0.0000653186791196846,
-    }
-
-
-def sample(
-    batch_id: str = "201860",
-    sample_id: str = "2020-07452-02",
-    ratio_13: float = 0.97,
-    ratio_18: float = 0.87,
-    fetal_fraction: float = 11.5,
-):
-    """A sample mock"""
-
-    return {
-        "_id": sample_id,
-        "SampleID": sample_id,
-        "SampleType": "",
-        "Description": "",
-        "SampleProject": batch_id,
-        "Index1": "CTACGAAG",
-        "Index2": "CTCGACAG",
-        "Library_nM": "",
-        "QCFlag": "",
-        "Zscore_13": 10.1836097044367,
-        "Zscore_18": 14.2869756828577,
-        "Zscore_21": 2.71403500910501,
-        "Zscore_X": 31.293635764028803,
-        "Ratio_13": ratio_13,
-        "Ratio_18": ratio_18,
-        "Ratio_21": 1.0105402184799999,
-        "Ratio_X": 0.85445334198,
-        "Ratio_Y": 0.0000711090401026516,
-        "MappedReads": 29855557,
-        "GC_Dropout": 0.000172,
-        "AT_Dropout": 44.723144,
-        "Chr1_Ratio": 0.992293808478,
-        "Chr2_Ratio": 1.0065908236399999,
-        "Chr3_Ratio": 0.974151095888,
-        "Chr4_Ratio": 1.10624166283,
-        "Chr5_Ratio": 1.0035390122299999,
-        "Chr6_Ratio": 1.03661992778,
-        "Chr7_Ratio": 1.0604126148100002,
-        "Chr8_Ratio": 0.987816483295,
-        "Chr9_Ratio": 1.00004978895,
-        "Chr10_Ratio": 0.984502658354,
-        "Chr11_Ratio": 0.949426097179,
-        "Chr12_Ratio": 1.0228564842799999,
-        "Chr14_Ratio": 0.988492203388,
-        "Chr15_Ratio": 0.9931196645579999,
-        "Chr16_Ratio": 0.9728049597669999,
-        "Chr17_Ratio": 1.04339140264,
-        "Chr19_Ratio": 1.05685913186,
-        "Chr20_Ratio": 0.917316392889,
-        "Chr22_Ratio": 1.05769882843,
-        "Chr1": 1641640,
-        "Chr2": 1456893,
-        "Chr3": 1089600,
-        "Chr4": 873556,
-        "Chr5": 968727,
-        "Chr6": 949012,
-        "Chr7": 1005851,
-        "Chr8": 851501,
-        "Chr9": 797378,
-        "Chr10": 949427,
-        "Chr11": 853961,
-        "Chr12": 853961,
-        "Chr13": 478503,
-        "Chr14": 593269,
-        "Chr15": 614267,
-        "Chr16": 749565,
-        "Chr17": 837952,
-        "Chr18": 439127,
-        "Chr19": 714656,
-        "Chr20": 555672,
-        "Chr21": 250072,
-        "Chr22": 451194,
-        "ChrX": 758991,
-        "ChrY": 2123,
-        "FF_Formatted": fetal_fraction,
-        "FFY": 0,
-        "FFX": 13.14,
-        "DuplicationRate": 0.0853080382992,
-        "Bin2BinVariance": 0.054260164076747,
-        "UnfilteredCNVcalls": 44,
-        "CNVSegment": "Found",
-        "comment": "None",
-    }
+@pytest.fixture(name="small_helpers")
+def fixture_small_helpers():
+    """Return a class with small helper functions"""
+    return SmallHelpers()
 
 
 ##########################################

diff --git a/tests/server/test_utils.py b/tests/server/test_utils.py
@@ -5,7 +5,6 @@
     get_statistics_for_scatter_plot,
 )
 from NIPTool.adapter.plugin import NiptAdapter
-from conftest import batch, sample
 from datetime import datetime
 
 
@@ -52,110 +51,49 @@ def test_get_last_batches_to_fiew_batches_in_database(database):
     assert results == [batch1, batch2, batch3, batch4]
 
 
-def test_get_statistics_for_box_plot(database):
+def test_get_statistics_for_box_plot(database, small_helpers):
     app.db = database
     app.adapter = NiptAdapter(database.client, db_name=database.name)
 
     # GIVEN a database with thre batches and nine samples like below
-    database.batch.insert_many(
-        [batch(batch_id="201860"), batch(batch_id="201861"), batch(batch_id="201862")]
-    )
-    database.sample.insert_many(
-        [
-            sample(
-                sample_id="07452-00",
-                batch_id="201860",
-                ratio_13=0.91,
-                fetal_fraction=10.5,
-            ),
-            sample(
-                sample_id="07452-01",
-                batch_id="201860",
-                ratio_13=0.92,
-                fetal_fraction=11.5,
-            ),
-            sample(
-                sample_id="07452-02",
-                batch_id="201860",
-                ratio_13=0.93,
-                fetal_fraction=12.5,
-            ),
-            sample(
-                sample_id="07452-03",
-                batch_id="201861",
-                ratio_13=0.94,
-                fetal_fraction=13.5,
-            ),
-            sample(
-                sample_id="07452-04",
-                batch_id="201861",
-                ratio_13=0.95,
-                fetal_fraction=14.5,
-            ),
-            sample(
-                sample_id="07452-05",
-                batch_id="201861",
-                ratio_13=0.96,
-                fetal_fraction=15.5,
-            ),
-            sample(
-                sample_id="07452-06",
-                batch_id="201862",
-                ratio_13=0.97,
-                fetal_fraction=16.5,
-            ),
-            sample(
-                sample_id="07452-07",
-                batch_id="201862",
-                ratio_13=0.98,
-                fetal_fraction=17.5,
-            ),
-            sample(
-                sample_id="07452-08",
-                batch_id="201862",
-                ratio_13=0.99,
-                fetal_fraction=18.5,
-            ),
-        ]
-    )
+    batches = ["201860", "201861", "201862"]
+    for batch_id in batches:
+        batch = small_helpers.batch(batch_id = batch_id)
+        database.batch.insert_one(batch)
+        for i in [1,2,3]:
+            sample = small_helpers.sample(
+                        sample_id = batch_id+str(i),
+                        batch_id = batch_id,
+                        ratio_13=i,
+                        fetal_fraction=i)
+            database.sample.insert_one(sample)
+
 
     # WHEN running get_statistics_for_box_plot
     results = get_statistics_for_box_plot(
         adapter=app.adapter,
-        batches=["201860", "201861", "201862"],
+        batches=batches,
         fields=["Ratio_13", "FF_Formatted"],
     )
 
     # THEN the results shoule be:
-    expected_result = [
-        {
-            "FF_Formatted": [10.5, 11.5, 12.5],
-            "Ratio_13": [0.91, 0.92, 0.93],
-            "_id": {"batch": "201860", "date": "2022-03-10"},
-        },
-        {
-            "FF_Formatted": [13.5, 14.5, 15.5],
-            "Ratio_13": [0.94, 0.95, 0.96],
-            "_id": {"batch": "201861", "date": "2022-03-10"},
-        },
-        {
-            "FF_Formatted": [16.5, 17.5, 18.5],
-            "Ratio_13": [0.97, 0.98, 0.99],
-            "_id": {"batch": "201862", "date": "2022-03-10"},
-        },
-    ]
-    assert results == expected_result
+    for index, result in enumerate(results):
+        assert result == {
+            "FF_Formatted": [1, 2, 3],
+            "Ratio_13": [1, 2, 3],
+            "_id": {"batch": batches[index], "date": "2022-03-10"},
+        }
 
 
-def test_get_statistics_for_scatter_plot(database):
+def test_get_statistics_for_scatter_plot(database, small_helpers):
     app.db = database
     app.adapter = NiptAdapter(database.client, db_name=database.name)
 
     # GIVEN a list with three batch documents:
     batches = [
-        batch(batch_id="201860", stdev_13=0.02, stdev_21=0.01),
-        batch(batch_id="201861", stdev_13=0.01, stdev_21=0.09),
-        batch(batch_id="201862", stdev_13=0.05, stdev_21=0.08),
+        small_helpers.batch(batch_id="201860", stdev_13=0.02, stdev_21=0.01),
+        small_helpers.batch(batch_id="201861", stdev_13=0.01, stdev_21=0.09),
+        small_helpers.batch(batch_id="201862", stdev_13=0.05, stdev_21=0.08),
     ]
 
     # WHEN running get_statistics_for_scatter_plot

diff --git a/tests/small_helpers.py b/tests/small_helpers.py
@@ -0,0 +1,114 @@
+"""Class with small helper functions"""
+
+
+class SmallHelpers:
+    """Hold small methods that might be helpful for the tests"""
+    @staticmethod
+    def batch(
+        batch_id="201860",
+        sequencing_date="2022-03-10",
+        stdev_13=0.0095,
+        stdev_18=0.0035,
+        stdev_21=0.0085,
+    ):
+        """A batch mock"""
+
+        return {
+            "_id": batch_id,
+            "SequencingDate": sequencing_date,
+            "Median_13": 0.994623404680424,
+            "Median_18": 1.01950547134618,
+            "Median_21": 1.00710552415657,
+            "Median_X": 0.8408228472301729,
+            "Median_Y": 0.00011224982090899999,
+            "Stdev_13": stdev_13,
+            "Stdev_18": stdev_18,
+            "Stdev_21": stdev_21,
+            "Stdev_X": 0.029800076293786,
+            "Stdev_Y": 0.0000653186791196846,
+        }
+
+    @staticmethod
+    def sample(
+        batch_id: str = "201860",
+        sample_id: str = "2020-07452-02",
+        ratio_13: float = 0.97,
+        ratio_18: float = 0.87,
+        fetal_fraction: float = 11.5,
+    ):
+        """A sample mock"""
+
+        return {
+            "_id": sample_id,
+            "SampleID": sample_id,
+            "SampleType": "",
+            "Description": "",
+            "SampleProject": batch_id,
+            "Index1": "CTACGAAG",
+            "Index2": "CTCGACAG",
+            "Library_nM": "",
+            "QCFlag": "",
+            "Zscore_13": 10.1836097044367,
+            "Zscore_18": 14.2869756828577,
+            "Zscore_21": 2.71403500910501,
+            "Zscore_X": 31.293635764028803,
+            "Ratio_13": ratio_13,
+            "Ratio_18": ratio_18,
+            "Ratio_21": 1.0105402184799999,
+            "Ratio_X": 0.85445334198,
+            "Ratio_Y": 0.0000711090401026516,
+            "MappedReads": 29855557,
+            "GC_Dropout": 0.000172,
+            "AT_Dropout": 44.723144,
+            "Chr1_Ratio": 0.992293808478,
+            "Chr2_Ratio": 1.0065908236399999,
+            "Chr3_Ratio": 0.974151095888,
+            "Chr4_Ratio": 1.10624166283,
+            "Chr5_Ratio": 1.0035390122299999,
+            "Chr6_Ratio": 1.03661992778,
+            "Chr7_Ratio": 1.0604126148100002,
+            "Chr8_Ratio": 0.987816483295,
+            "Chr9_Ratio": 1.00004978895,
+            "Chr10_Ratio": 0.984502658354,
+            "Chr11_Ratio": 0.949426097179,
+            "Chr12_Ratio": 1.0228564842799999,
+            "Chr14_Ratio": 0.988492203388,
+            "Chr15_Ratio": 0.9931196645579999,
+            "Chr16_Ratio": 0.9728049597669999,
+            "Chr17_Ratio": 1.04339140264,
+            "Chr19_Ratio": 1.05685913186,
+            "Chr20_Ratio": 0.917316392889,
+            "Chr22_Ratio": 1.05769882843,
+            "Chr1": 1641640,
+            "Chr2": 1456893,
+            "Chr3": 1089600,
+            "Chr4": 873556,
+            "Chr5": 968727,
+            "Chr6": 949012,
+            "Chr7": 1005851,
+            "Chr8": 851501,
+            "Chr9": 797378,
+            "Chr10": 949427,
+            "Chr11": 853961,
+            "Chr12": 853961,
+            "Chr13": 478503,
+            "Chr14": 593269,
+            "Chr15": 614267,
+            "Chr16": 749565,
+            "Chr17": 837952,
+            "Chr18": 439127,
+            "Chr19": 714656,
+            "Chr20": 555672,
+            "Chr21": 250072,
+            "Chr22": 451194,
+            "ChrX": 758991,
+            "ChrY": 2123,
+            "FF_Formatted": fetal_fraction,
+            "FFY": 0,
+            "FFX": 13.14,
+            "DuplicationRate": 0.0853080382992,
+            "Bin2BinVariance": 0.054260164076747,
+            "UnfilteredCNVcalls": 44,
+            "CNVSegment": "Found",
+            "comment": "None",
+        }