From 87caba4039e75aefae905017820dac0116fd9f13 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Mon, 4 Dec 2023 15:08:22 +0100
Subject: [PATCH] add unit tests for `Spectrum` class

---
 tests/metabolomics/test_spectrum.py | 70 ++++++++++++++++++++++++++---
 1 file changed, 64 insertions(+), 6 deletions(-)

diff --git a/tests/metabolomics/test_spectrum.py b/tests/metabolomics/test_spectrum.py
index e039197a..689f9c25 100644
--- a/tests/metabolomics/test_spectrum.py
+++ b/tests/metabolomics/test_spectrum.py
@@ -1,12 +1,70 @@
+import numpy as np
 import pytest
 from nplinker.metabolomics import Spectrum
+from nplinker.strain import Strain
+from nplinker.strain_collection import StrainCollection
 
 
-@pytest.fixture
-def spectrum() -> Spectrum:
-    spec = Spectrum(spectrum_id="2", mz=[10, 20], intensity=[100, 150], precursor_mz=30, rt=100)
-    return spec
+@pytest.mark.parametrize(
+    "rt, metadata, expected_metadata",
+    [
+        [0, None, {}],
+        [1, {"info": "test"}, {"info": "test"}],
+    ],
+)
+def test_init(rt, metadata, expected_metadata):
+    """Test the initialization of the Spectrum class."""
+    spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150, rt, metadata)
 
+    assert spec.spectrum_id == "spec1"
+    assert spec.mz == [100, 200]
+    assert spec.intensity == [0.1, 0.2]
+    assert spec.precursor_mz == 150
+    assert spec.rt == rt
+    assert spec.metadata == expected_metadata
 
-def test_constructor(spectrum):
-    assert spectrum is not None
+    # test the default values of the attributes
+    assert spec.gnps_annotations == {}
+    assert spec.gnps_id is None
+    assert spec.strains == StrainCollection()
+    assert spec.family is None
+
+
+def test_str_repr():
+    """Test the __str__ and __repr__ methods."""
+    spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150)
+    assert str(spec) == "Spectrum(spectrum_id=spec1, #strains=0)"
+    assert repr(spec) == "Spectrum(spectrum_id=spec1, #strains=0)"
+
+
+def test_eq():
+    """Test the __eq__ method."""
+    spec1 = Spectrum("spec1", [100, 200], [0.1, 0.2], 150, 0, {"info": "test"})
+    spec2 = Spectrum("spec1", [100, 200], [0.1, 0.2], 150, 0, {"info": "test"})
+    spec3 = Spectrum("spec2", [100, 200], [0.1, 0.2], 150, 0, {"info": "test"})
+
+    assert spec1 == spec2
+    assert spec1 != spec3
+
+
+def test_hash():
+    """Test the __hash__ method."""
+    spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150)
+    assert hash(spec) == hash(("spec1", 150))
+
+
+def test_peaks():
+    """Test the peaks attribute."""
+    spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150)
+    assert np.array_equal(spec.peaks, np.array([[100, 0.1], [200, 0.2]]))
+
+
+def test_has_strain():
+    """Test the has_strain method."""
+    spec = Spectrum("spec1", [100, 200], [0.1, 0.2], 150)
+    strain1 = Strain("strain1")
+    strain2 = Strain("strain2")
+
+    spec.strains.add(strain1)
+    assert spec.has_strain(strain1)
+    assert not spec.has_strain(strain2)