From 49455485131537e9f5fb9d553160b3ee58ac1c26 Mon Sep 17 00:00:00 2001
From: Martin Beracochea <mbc@ebi.ac.uk>
Date: Wed, 21 Feb 2024 21:40:20 +0000
Subject: [PATCH] Add one more unit test for amplicon_utils_tests

---
 .gitignore                                    |  1 +
 .../analysis/amplicon/amplicon_utils.py       |  4 +-
 .../analysis/amplicon/amplicon_utils_tests.py | 68 +++++++++++++++++++
 3 files changed, 71 insertions(+), 2 deletions(-)
 create mode 100644 tests/unit/analysis/amplicon/amplicon_utils_tests.py

diff --git a/.gitignore b/.gitignore
index b4aea5a..a86b0c3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 dist/
 *.egg-info/
 __pycache__/
+build/
\ No newline at end of file
diff --git a/mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py b/mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py
index 2054bbc..155182e 100644
--- a/mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py
+++ b/mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py
@@ -70,10 +70,10 @@ def get_read_count(read_path, type='fastq'):
         grep_proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         stdout, stderr = grep_proc.communicate()
 
-    read_count = stdout.strip()
+    read_count = stdout.strip() if stdout is not None else "" 
 
     if not read_count.isdigit():
-        logging.error("Read count is not a digit, something wrong.")
+        logging.error(f"Read count is not a digit, something is wrong. stdout: '{stdout}', stderr: '{stderr}'")
         exit(1)
 
     read_count = int(read_count)
diff --git a/tests/unit/analysis/amplicon/amplicon_utils_tests.py b/tests/unit/analysis/amplicon/amplicon_utils_tests.py
new file mode 100644
index 0000000..7cfb745
--- /dev/null
+++ b/tests/unit/analysis/amplicon/amplicon_utils_tests.py
@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright 2024 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from unittest.mock import patch
+
+import pytest
+
+from mgnify_pipelines_toolkit.analysis.amplicon.amplicon_utils import get_read_count
+
+
+@pytest.mark.parametrize(
+    "read_count_output, expected_result",
+    [
+        ("123\n", 123),
+        ("5435", 5435),
+        ("1000000000000", 1000000000000),
+        ("999999999999999999999999999999", 999999999999999999999999999999),
+        ("\n999999999999999999999999999999", 999999999999999999999999999999),
+        ("\n999999999999999999999999999999\n", 999999999999999999999999999999),
+        ("     999999999999999999999999999999      ", 999999999999999999999999999999),
+    ],
+)
+@patch("mgnify_pipelines_toolkit.analysis.amplicon.amplicon_utils.subprocess.Popen")
+def test_get_read_count(mock_popen, read_count_output, expected_result):
+    mock_process = mock_popen.return_value
+    mock_process.communicate.return_value = (read_count_output, expected_result)
+
+    print(expected_result)
+
+    read_count = get_read_count("/path/to/read_file")
+
+    assert read_count == expected_result
+
+
+@pytest.mark.parametrize(
+    "read_count_output",
+    [
+        "9999.9999",
+        "abc\n",
+        "",
+        None,
+        "8765\t888",
+        "888 888",
+    ],
+)
+@patch("mgnify_pipelines_toolkit.analysis.amplicon.amplicon_utils.subprocess.Popen")
+def test_get_read_count_error(mock_popen, read_count_output):
+    mock_process = mock_popen.return_value
+    mock_process.communicate.return_value = (read_count_output, None)
+    # Simulating non-digit output
+    with pytest.raises(SystemExit) as exc_info:
+        get_read_count("/path/to/read_file")
+
+    assert exc_info.type == SystemExit
+    assert exc_info.value.code == 1