streamlines read_molecule_file logic

propka/input.py

@@ -35,13 +35,15 @@ def open_file_for_reading(input_file):
     return file_
 
 
-def read_molecule_file(input_file, mol_container, filename=None):
+def read_molecule_file(filename: str, mol_container, stream=None):
     """Read input file or stream (PDB or PROPKA) for a molecular container
 
     Args:
-        input_file:  input file or stream to read
+        filename(str):  name of input file. If not using a filestream via the
-        mol_container:  MolecularContainer object
+            ``stream`` argument, should be a path to the file to be read.
-        filename (str): optional input filename when using a filestream
+        mol_container:  MolecularContainer object.
+        stream: optional filestream handle. If ``None``, then open
+            ``filename`` as a local file for reading.
 
     Returns:
         updated MolecularContainer object
@@ -51,7 +53,7 @@ def read_molecule_file(input_file, mol_container, filename=None):
 
     Examples:
         There are two main cases for using ``read_molecule_file``. The first
-        (and most common) is to pass the input file (``input_file``) as a
+        (and most common) is to pass the input file (``filename``) as a
         string which gives the path of the molecule file to be read (here we
         also pass a ``MoleculeContainer`` object named ``mol_container``).
 
@@ -59,39 +61,36 @@ def read_molecule_file(input_file, mol_container, filename=None):
         <propka.molecular_container.MolecularContainer at 0x7f6e0c8f2310>
 
         The other use case is when passing a file-like object, e.g. a
-        ``StringIO`` class, instance as the input file. In order to decide how
+        ``StringIO`` class, instance. This is done by passing the object via
-        to process ``input_file``, ``read_molecule_file`` requires a file name.
+        the ``stream`` argument. Since file-like objects do not usually have
-        Since file-like objects do not usually have an associated file name, we
+        an associated file name, an appropirate file name should be passed to
-        must pass a value to the ``filename`` argument. This helps recognise
+        the ``filename`` argument. In this case, ``filename`` is not opened for
-        the file type (based on the extension being either `.pdb` or
+        reading, but instead is used to help recognise the file type (based on
-        `.propka_input`) and also associates that given ``filename`` with the
+        the extension being either `.pdb` or `.propka_input`) and also uses
-        input MolecularContainer object.
+        that given ``filename`` to assign a name to the input
+        MolecularContainer object.
 
-        >>> read_molecule_file(string_io_object, mol_container,
+        >>> read_molecule_file('test.pdb', mol_container,
-                               filename='test.pdb')
+                               stream=string_io_object)
         <propka.molecular_container.MolecularContainer at 0x7f6e0c8f2310>
 
     """
-    try:
+    input_path = Path(filename)
-        input_path = Path(input_file)
-    except TypeError:
-        try:
-            input_path = Path(filename)
-        except TypeError:
-            errmsg = ("Path of provided input_file could not be determined "
-                      "if passing a stream-like object, please provide an "
-                      "appropriate string for the filename argument.")
-            raise TypeError(errmsg) from None
-
     mol_container.name = input_path.stem
     input_file_extension = input_path.suffix
+
+    if stream is not None:
+        input_file = stream
+    else:
+        input_file = filename
+
     if input_file_extension.lower() == '.pdb':
         # input is a pdb file. read in atoms and top up containers to make
         # sure that all atoms are present in all conformations
         conformations, conformation_names = read_pdb(
             input_file, mol_container.version.parameters, mol_container)
         if len(conformations) == 0:
-            str_ = ('Error: The pdb file does not seems to contain any '
+            str_ = ('Error: The pdb file does not seem to contain any '
                     'molecular conformations')
             raise ValueError(str_)
         mol_container.conformations = conformations

tests/test_streamio.py

@@ -30,13 +30,12 @@ def run_propka_stream(options, input_file, filename):
         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 = read_molecule_file(filename, molecule, stream=input_file)
     molecule.calculate_pka()
     molecule.write_pka()
     if args.generate_propka_input:
@@ -90,9 +89,9 @@ def test_stringio_filestream(tmpdir, pdb, options):
     filestream.close()
 
 
-def test_typerror_nofilename(tmpdir):
+def test_valuerror_nofiletype(tmpdir):
-    """Tests for raised TypeError when not passing a filename to
+    """Tests for raised ValueError when an unknown filename is passed to
-    read_molecule_file and using a file-like object without a name"""
+    read_molecule_file"""
     pdb = "1FTJ-Chain-A"
     options = []
 
@@ -101,8 +100,22 @@ def test_typerror_nofilename(tmpdir):
     with open(pdb_path, 'r') as writer:
         filestream = StringIO(writer.read())
 
-    with tmpdir.as_cwd():
+    errmsg = "Unknown input file type"
-        errmsg = "Path of provided input_file could not be determined"
+    with pytest.raises(ValueError, match=errmsg):
-        with pytest.raises(TypeError, match=errmsg):
+        run_propka_stream(options, filestream, filename="test.dat")
-            # default value of filename is None
+
-            run_propka_stream(options, filestream, filename=None)
+
+def test_valuerror_notpdb(tmpdir):
+    """Tests for raised ValueError when a stream object that isn't a PDB
+    is passed to read_molecule_file"""
+    pdb = "1FTJ-Chain-A"
+    options = []
+
+    ref_path, pdb_path = get_paths(pdb)
+
+    with open(pdb_path, 'r') as writer:
+        filestream = StringIO()
+
+    errmsg = "The pdb file does not seem to contain any "
+    with pytest.raises(ValueError, match=errmsg):
+        run_propka_stream(options, filestream, filename="test.pdb")