diff tests/test_imgt.py @ 56:7ae6b6b5d890 draft

"planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/test_imgt.py	Tue Dec 14 12:45:47 2021 +0000
@@ -0,0 +1,89 @@
+# 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 tempfile
+from pathlib import Path
+from xml.etree import ElementTree
+from xml.etree.ElementTree import Element
+
+import pytest
+
+GIT_ROOT = 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"
+
+
+def get_container():
+    tool = ElementTree.parse(GIT_ROOT / "complete_immunerepertoire.xml").getroot()
+    requirements: Element = tool.find("requirements")
+    container = requirements.find("container")
+    return container.text
+
+
[e-mail](scope="module")
+def imgt_result():
+    temp_dir = Path(tempfile.mkdtemp())
+    tool_dir = temp_dir / "imgt"
+    shutil.copytree(GIT_ROOT, tool_dir)
+    working_dir = temp_dir / "working"
+    working_dir.mkdir(parents=True)
+    output_dir = temp_dir / "outputs"
+    output_dir.mkdir(parents=True)
+    wrapper = str(tool_dir / "complete.sh")
+    sample = CONTROL_NWK377_PB_IGHC_MID1_40nt_2
+    input = f"\"ID1\" {sample} {sample} \"ID2\" {sample}"
+    out_files_path = output_dir / "results"
+    out_files_path.mkdir(parents=True)
+    out_file = out_files_path / "result.html"
+    clonaltype = "none"
+    gene_selection = dict(species="Homo sapiens functional",
+                          locus="TRA")
+    filterproductive = "yes"
+    clonality_method = "none"
+    cmd = [
+        "bash",
+        wrapper,
+        input,
+        str(out_file),
+        str(out_files_path),
+        clonaltype,
+        gene_selection["species"],
+        gene_selection["locus"],
+        filterproductive,
+        clonality_method
+    ]
+    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
+                  "-v", f"{sample}:{sample}",
+                  "-w", str(working_dir),
+                  get_container()] + cmd
+    with open(temp_dir / "stderr", "wt") as stderr_file:
+        with open(temp_dir / "stdout", "wt") as stdout_file:
+            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
+                           stderr=stderr_file, check=True)
+    yield Path(out_files_path)
+
+
+def test_check_output(imgt_result):
+    assert imgt_result.exists()