Add testing for FilePath.run and environment variable options

test/test_file_path.py

@@ -1,22 +1,125 @@
+import os
+
 from em_workflows.file_path import FilePath
+from pathlib import Path
+import sys
 
 
 def test_gen_output_fp(mock_nfs_mount, tmp_path):
-    input_dir = tmp_path / "Projects"
-    input_dir.mkdir()
-    p = input_dir / "some_file_rec.mrc"
-    p.write_text("content")
-    assert str(p).endswith("Projects/some_file_rec.mrc")
+    input_dir = Path("test/input_files/brt/Projects/2013-1220-dA30_5-BSC-1_10.mrc").absolute()
+
+    file_base_name = input_dir.stem
 
-    fp_in = FilePath(share_name="test", input_dir=input_dir, fp_in=p)
+    fp_in = FilePath(share_name="test", input_dir=input_dir.parent, fp_in=input_dir)
 
     zarr = fp_in.gen_output_fp(output_ext=".zarr")
     rec_mrc = fp_in.gen_output_fp(output_ext="_rec.mrc")
     base_mrc = fp_in.gen_output_fp(output_ext=".mrc", out_fname="adjusted.mrc")
     input_mrc = fp_in.fp_in
     print(f"{rec_mrc=}\n{base_mrc=}\n{input_mrc=}")
-    assert zarr.name == "some_file_rec.zarr"
+    assert zarr.name == f"{file_base_name}.zarr"
     assert base_mrc.name == "adjusted.mrc"
-    assert input_mrc.name == "some_file_rec.mrc"
+    assert input_mrc.name == f"{file_base_name}.mrc"
     # Below is simply a temporary outfile loc
-    assert rec_mrc.name == "some_file_rec_rec.mrc"
+    assert rec_mrc.name == f"{file_base_name}_rec.mrc"
+
+
+# Test the FilePath.run function by executing the python shell, and producing putput to stderr and stdout
+def test_filepath_run(mock_nfs_mount, tmp_path, request):
+    current_test_name = request.node.name
+    log_file = tmp_path/f"{current_test_name}.log"
+
+    input_filename = "test/input_files/dm_inputs/Projects/Lab/PI/PrP - Protein.007.tif"
+    input_dir = Path(input_filename).absolute()
+
+    fp_in = FilePath(share_name="test", input_dir=input_dir.parent, fp_in=input_dir)
+
+    # Run the python shell, and produce output to stderr and stdout
+    cmd = [sys.executable, "-c", "import sys; print('stdout'); print('stderr', file=sys.stderr)"]
+    fp_in.run(cmd, log_file=str(log_file))
+
+    # Check if the log file was created
+    assert log_file.exists()
+
+    # Check that the log contain "stdout" and "stderr" strings
+    with open(log_file, "r") as f:
+        log_content = f.read()
+        assert "stdout" in log_content
+        assert "stderr" in log_content
+
+
+# Write a pytest for FilePath.run function by executing the python shell which print the environment variables.
+# Combinations of setting the "env" parameter and "copy_env" need to be tested.
+def test_filepath_run_env(mock_nfs_mount, tmp_path, request):
+    current_test_name = request.node.name
+    log_file = tmp_path/f"{current_test_name}.log"
+
+    input_filename = "test/input_files/dm_inputs/Projects/Lab/PI/PrP - Protein.007.tif"
+    input_dir = Path(input_filename).absolute()
+
+    fp_in = FilePath(share_name="test", input_dir=input_dir.parent, fp_in=input_dir)
+
+    os.environ["PARENT_ENV"] = "parent_env_value"
+
+    # Case 1: env is set, and copy_env is set to False
+
+    # Run the python shell, and print all environment variables
+    cmd = [sys.executable, "-c", "import os; print(os.environ)"]
+    fp_in.run(cmd, log_file=str(log_file), env={"ENV_VAR": "env_var_value"}, copy_env=False)
+
+    # Check if the log file was created
+    assert log_file.exists()
+
+    with open(log_file, "r") as f:
+        log_content = f.read()
+        assert "env_var_value" in log_content
+        assert "parent_env_value" not in log_content
+    log_file.unlink()
+
+    # Case 2: env is set, and copy_env is set to True
+
+    # Run the python shell, and print all environment variables
+    cmd = [sys.executable, "-c", "import os; print(os.environ)"]
+    fp_in.run(cmd, log_file=str(log_file), env={"ENV_VAR": "env_var_value"}, copy_env=True)
+
+    # Check if the log file was created
+    assert log_file.exists()
+
+    # Check that the log contain "env_var_value" string
+    with open(log_file, "r") as f:
+        log_content = f.read()
+        assert "env_var_value" in log_content
+        assert "parent_env_value" in log_content
+    log_file.unlink()
+
+    # Case 3: env is not set, and copy_env is set to False
+
+    # Run the python shell, and print all environment variables
+    cmd = [sys.executable, "-c", "import os; print(os.environ)"]
+    fp_in.run(cmd, log_file=str(log_file), env=None, copy_env=True)
+
+    # Check if the log file was created
+    assert log_file.exists()
+
+    # Check that the log contain "env_var_value" string
+    with open(log_file, "r") as f:
+        log_content = f.read()
+        assert "env_var_value" not in log_content
+        assert "parent_env_value" in log_content
+    log_file.unlink()
+
+    # Case 4: env is not set, and copy_env is set to False
+
+    # Run the python shell, and print all environment variables
+    cmd = [sys.executable, "-c", "import os; print(os.environ)"]
+    fp_in.run(cmd, log_file=str(log_file), env=None, copy_env=False)
+
+    # Check if the log file was created
+    assert log_file.exists()
+
+    # Check that the log contain "env_var_value" string
+    with open(log_file, "r") as f:
+        log_content = f.read()
+        assert "env_var_value" not in log_content
+        assert "parent_env_value" not in log_content
+    log_file.unlink()