added tests for serialization.py

README.md

@@ -228,7 +228,7 @@ The first entry in the list should be the type of files the experiments contain,
 followed by the type in quotation marks. The type can be either `fastq` or `bam`.
 
 Each experiment is represented as set of parameters (e.g. in curly brackets).
-Each experiment must have a name and a list if long-read files in the specified format.
+Each experiment must have a name and a list of long-read files in the specified format.
 Additionally, it may contain one or multiple BAM files with short reads.
 The name is provided as `name: ` followed by the experiment name in quotation marks.
 Both short and long read files are provided as a list of file paths in quotation marks,

src/serialization.py

@@ -1,4 +1,3 @@
-
 ############################################################################
 # Copyright (c) 2022-2024 University of Helsinki
 # All Rights Reserved
@@ -109,6 +108,7 @@ def read_bool_array(inf, arr_size=1):
     return bool_arr
 
 
+# transforms a signed integer into an unsigned integer while using the 31st bit as a flag to remember the original sign
 def write_int_neg(val, outf):
     if val < 0:
         val = abs(val)

tests/test_serialization.py

@@ -0,0 +1,103 @@
+import os
+
+import pytest
+
+from src import serialization
+
+filename = "ser_test_file"
+
+
+@pytest.fixture(scope="class")
+def setup_class(request):
+    request.cls.filehandler = open(filename, "xb")
+    yield
+    os.remove(filename)
+
+
+@pytest.fixture(autouse=True)
+def run_after_each_test(request):
+    request.cls.filehandler = open(filename, "r+b")
+    yield
+    request.cls.filehandler.close()
+
+
+@pytest.mark.usefixtures("setup_class")
+class TestSerialization:
+
+    @pytest.mark.parametrize(
+        "func_wr, func_rd, value",
+        [
+            (serialization.write_int, serialization.read_int, 1),
+            (serialization.write_int, serialization.read_int, 0),
+            (serialization.write_int, serialization.read_int, 65536),
+            (serialization.write_short_int, serialization.read_short_int, 0),
+            (serialization.write_short_int, serialization.read_short_int, 65535),
+            (serialization.write_string, serialization.read_string, ""),
+            (serialization.write_string, serialization.read_string, "quite a long string dont you think"),
+            (serialization.write_string_or_none, serialization.read_string_or_none, None),
+            (serialization.write_string_or_none, serialization.read_string_or_none, "None"),
+            (serialization.write_int_neg, serialization.read_int_neg, -1),
+            (serialization.write_int_neg, serialization.read_int_neg, -65536),
+            (serialization.write_bool_array, serialization.read_bool_array, [False]),
+            (serialization.write_dict, serialization.read_dict, {'key1': 'value1', 'key2': 'value2'}),
+            (serialization.write_dict, serialization.read_dict, {'key1': 0, 'key2': (655536, 1)}),
+            (serialization.write_dict, serialization.read_dict, {})
+        ]
+    )
+    def test_write_read_positive(self, value, func_wr, func_rd):
+        func_wr(value, self.filehandler)
+        self.filehandler.flush()
+        self.filehandler.seek(0)
+        actual = func_rd(self.filehandler)
+        assert actual == value
+
+    @pytest.mark.parametrize(
+        "func_wr, func_rd, value",
+        [
+            (serialization.write_int, serialization.read_int, [65539, 0, 1]),
+            (serialization.write_int, serialization.read_int, []),
+            (serialization.write_string_or_none, serialization.read_string_or_none, ["str", "", None]),
+            (serialization.write_string_or_none, serialization.read_string_or_none, []),
+            (serialization.write_string, serialization.read_string, ["str", "quite a long string dont you think", ""]),
+            (serialization.write_string, serialization.read_string, []),
+            (serialization.write_int_neg, serialization.read_int_neg, [-6, -33333, 0]),
+            (serialization.write_int_neg, serialization.read_int_neg, [])
+        ]
+    )
+    def test_write_read_lists_positive(self, func_wr, func_rd, value):
+        serialization.write_list(value, self.filehandler, func_wr)
+        self.filehandler.flush()
+        self.filehandler.seek(0)
+        actual = serialization.read_list(self.filehandler, func_rd)
+        assert actual == value
+
+    @pytest.mark.parametrize(
+        "value",
+        [
+            ([]),
+            ([True, False]),
+            ([False, False, False, True, False, True, True, False]),
+        ]
+    )
+    def test_write_read_bool_array_positive(self, value):
+        serialization.write_bool_array(value, self.filehandler)
+        self.filehandler.flush()
+        self.filehandler.seek(0)
+        actual = serialization.read_bool_array(self.filehandler, len(value))
+        assert actual == value
+
+    @pytest.mark.parametrize(
+        "func_wr, func_rd, list_of_pairs",
+        [
+            (serialization.write_int, serialization.read_int, []),
+            (serialization.write_int, serialization.read_int, [(1225, 78854)]),
+            (serialization.write_int, serialization.read_int, [(1225, 78854), (1, 0), (65536, 65536)]),
+            (serialization.write_string, serialization.read_string, [("1225", "78854"), ("", " "), ("65536", "65536")])
+        ]
+    )
+    def test_write_read_list_of_pairs_positive(self, func_wr, func_rd, list_of_pairs):
+        serialization.write_list_of_pairs(list_of_pairs, self.filehandler, func_wr)
+        self.filehandler.flush()
+        self.filehandler.seek(0)
+        actual = serialization.read_list_of_pairs(self.filehandler, func_rd)
+        assert actual == list_of_pairs