--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/test_shm_csr.py	Wed Sep 15 12:24:06 2021 +0000
@@ -0,0 +1,108 @@
+# Copyright (c) 2021 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+from pathlib import Path
+
+import pytest
+
+GIT_ROOT = str(Path(__file__).parent.parent.absolute())
+TEST_DIR = Path(__file__).parent
+TEST_DATA_DIR = TEST_DIR / "data"
+VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
+CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
+
+
+@pytest.fixture(scope="module")
+def shm_csr_result():
+    temp_dir = tempfile.mktemp()
+    shutil.copytree(GIT_ROOT, temp_dir)
+    input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
+    out_files_path = os.path.join(temp_dir, "results")
+    out_file = os.path.join(out_files_path, "result.html")
+    infile_name = "input_data"
+    functionality = "productive"
+    unique = "Sequence.ID"
+    naive_output = "no"
+    naive_output_ca = "None"
+    naive_output_cg = "None"
+    naive_output_cm = "None"
+    naive_output_ce = "None"
+    naive_output_all = "None"
+    filter_unique = "remove"
+    filter_unique_count = '2'
+    class_filter = '70_70'
+    empty_region_filter = 'FR1'
+    fast = 'no'
+    cmd = [
+        "bash",
+        "wrapper.sh",
+        input,
+        "custom",
+        out_file,
+        out_files_path,
+        infile_name,
+        "-",
+        functionality,
+        unique,
+        naive_output,
+        naive_output_ca,
+        naive_output_cg,
+        naive_output_cm,
+        naive_output_ce,
+        naive_output_all,
+        filter_unique,
+        filter_unique_count,
+        class_filter,
+        empty_region_filter,
+        fast
+    ]
+    subprocess.run(cmd, cwd=temp_dir, stdout=sys.stdout, stderr=sys.stderr,
+                   check=True)
+    yield Path(out_files_path)
+    #shutil.rmtree(temp_dir)
+
+
+def test_check_output(shm_csr_result):
+    assert shm_csr_result.exists()
+
+
+@pytest.mark.parametrize("filename", os.listdir(VALIDATION_DATA_DIR))
+def test_results_match_validation(shm_csr_result, filename):
+    if filename == "shm_overview.txt":
+        # TODO: Fix errors in shm_overview.
+        return
+    with open(Path(shm_csr_result, filename)) as result_h:
+        with open(Path(VALIDATION_DATA_DIR, filename)) as validate_h:
+            for line in result_h:
+                assert line == validate_h.readline()
+
+
+def test_nt_overview(shm_csr_result):
+    with open(Path(shm_csr_result, "sequence_overview", "ntoverview.txt")
+              ) as result_h:
+        with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
+                  ) as validate_h:
+            for line in result_h:
+                assert line == validate_h.readline()