stringio tests

propka/input.py

@@ -20,7 +20,7 @@ def open_file_for_reading(input_file):
 
     Args:
         input_file: path to file or file-like object. If file-like object,
-        then will attempt fseek(0).
+        then will attempt seek(0).
     """
     try:
         input_file.seek(0)
@@ -36,7 +36,7 @@ def open_file_for_reading(input_file):
 
 
 def read_molecule_file(input_file, mol_container, filename=None):
-    """Read input file (PDB or PROPKA) for a molecular container
+    """Read input file or stream (PDB or PROPKA) for a molecular container
 
     Args
         input_file:  input file to read

tests/__init__.py

@@ -0,0 +1 @@
+

tests/test_basic_regression.py

@@ -3,6 +3,7 @@ import logging
 import os
 import re
 from pathlib import Path
+from io import StringIO
 import pytest
 from numpy.testing import assert_almost_equal
 from propka.parameters import Parameters
@@ -154,7 +155,7 @@ def test_regression(pdb, options, tmp_path):
         compare_output(pdb, tmp_path, ref_path)
 
 
-def run_propka_stream(options, input_file, tmp_path):
+def run_propka_stream(options, input_file, filename, tmp_path):
     """Run PROPKA software.
 
     Args:
@@ -162,7 +163,7 @@ def run_propka_stream(options, input_file, tmp_path):
         input_file:  file-like PDB object
         tmp_path:  path for working directory
     """
-    options += [input_file.name]
+    options += [filename]
     args = loadOptions(options)
     try:
         _LOGGER.warning(
@@ -173,7 +174,7 @@ def run_propka_stream(options, input_file, tmp_path):
         parameters = read_parameter_file(args.parameters, Parameters())
         molecule = MolecularContainer(parameters, args)
         molecule = read_molecule_file(input_file, molecule,
-                                      filename=input_file.name)
+                                      filename=filename)
         molecule.calculate_pka()
         molecule.write_pka()
         if args.generate_propka_input:
@@ -205,14 +206,15 @@ def test_filestream_regression(pdb, options, tmp_path):
     pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
     if pdb_path.is_file():
         pdb_path = pdb_path.resolve()
-        input_file = open(pdb_path)
+        #input_file = open(pdb_path)
+        with open(pdb_path, 'r') as writer:
+            io_file = StringIO(writer.read())
     else:
         errstr = "Missing PDB file: {0:s}".format(pdb_path)
         raise FileNotFoundError(errstr)
     tmp_path = Path(tmp_path).resolve()
 
-    run_propka_stream(options, input_file, tmp_path)
+    run_propka_stream(options, io_file, f"{pdb}.pdb", tmp_path)
 
     if ref_path is not None:
         compare_output(pdb, tmp_path, ref_path)
-    input_file.close()

tests/test_streamio.py

@@ -0,0 +1,108 @@
+"""Tests for PROPKA stream io"""
+import logging
+from pathlib import Path
+from io import StringIO
+import pytest
+from propka.parameters import Parameters
+from propka.molecular_container import MolecularContainer
+from propka.input import read_parameter_file, read_molecule_file
+from propka.lib import loadOptions
+
+from .test_basic_regression import get_test_dirs, compare_output
+
+
+_LOGGER = logging.getLogger(__name__)
+
+
+def get_paths(pdb):
+    """Helper function to get the path to the input and reference files"""
+    path_dict = get_test_dirs()
+    ref_path = path_dict["results"] / ("{0:s}.dat".format(pdb))
+    pdb_path = path_dict["pdbs"] / ("{0:s}.pdb".format(pdb))
+
+    return ref_path.resolve(), pdb_path.resolve()
+
+
+def run_propka_stream(options, input_file, filename):
+    """Run PROPKA software.
+
+    Args:
+        options:  list of PROPKA options
+        input_file:  file-like PDB object
+        filename: filename for the file-like PDB object
+        tmp_path:  path for working directory
+    """
+    options += [filename]
+    args = loadOptions(options)
+    parameters = read_parameter_file(args.parameters, Parameters())
+    molecule = MolecularContainer(parameters, args)
+    molecule = read_molecule_file(input_file, molecule, filename)
+    molecule.calculate_pka()
+    molecule.write_pka()
+    if args.generate_propka_input:
+        molecule.write_propka()
+
+
+@pytest.mark.parametrize("pdb, options", [
+    pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"),
+    pytest.param('3SGB-subset', [
+        "--titrate_only",
+        "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"],
+                 id="3SGB: --titrate_only"),
+    pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"),
+])
+def test_textio_filestream(tmpdir, pdb, options):
+    """Basic regression test using TextIO streams for the input PDB file"""
+    # Get the relevant paths
+    ref_path, pdb_path = get_paths(pdb)
+    filename = f"{pdb}.pdb"
+
+    filestream = open(pdb_path, 'r')
+
+    with tmpdir.as_cwd():
+        run_propka_stream(options, filestream, filename)
+        compare_output(pdb, Path.cwd(), ref_path)
+
+    filestream.close()
+
+
+@pytest.mark.parametrize("pdb, options", [
+    pytest.param("1FTJ-Chain-A", [], id="1FTJ-Chain-A: no options"),
+    pytest.param('3SGB-subset', [
+        "--titrate_only",
+        "E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139"],
+                 id="3SGB: --titrate_only"),
+    pytest.param('1HPX-warn', ['--quiet'], id="1HPX-warn: --quiet"),
+])
+def test_stringio_filestream(tmpdir, pdb, options):
+    """Basic regression test using StringIO streams for the input PDB file"""
+    # Get the relevant paths
+    ref_path, pdb_path = get_paths(pdb)
+    filename = f"{pdb}.pdb"
+
+    with open(pdb_path, 'r') as writer:
+        filestream = StringIO(writer.read())
+
+    with tmpdir.as_cwd():
+        run_propka_stream(options, filestream, filename)
+        compare_output(pdb, Path.cwd(), ref_path)
+
+    filestream.close()
+
+
+def test_typerror_nofilename(tmpdir):
+    """Tests for raised TypeError when not passing a filename to
+    read_molecule_file and using a file-like object without a name"""
+    pdb = "1FTJ-Chain-A"
+    options = []
+
+    ref_path, pdb_path = get_paths(pdb)
+
+    with open(pdb_path, 'r') as writer:
+        filestream = StringIO(writer.read())
+
+    with tmpdir.as_cwd():
+        errmsg = "Path of provided input_file could not be determined"
+        with pytest.raises(TypeError, match=errmsg):
+            # default value of filename is None
+            run_propka_stream(options, filestream, filename=None)