Merge branch 'master' of ssh://github.com/KarrLab/wc_utils

tests/util/test_files.py

@@ -1,6 +1,7 @@
 """ Tests of the file utilities
 
 :Author: Jonathan Karr <jonrkarr@gmail.com>
+:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
 :Date: 2018-05-11
 :Copyright: 2018, Karr Lab
 :License: MIT
@@ -11,9 +12,12 @@
 import shutil
 import tempfile
 import unittest
+import getpass
+from pathlib import Path
 
 
 class FileUtilsTestCase(unittest.TestCase):
+
     def setUp(self):
         self.dirname = tempfile.mkdtemp()
 
@@ -60,3 +64,36 @@ def test_copytree_to_existing_destination(self):
         files.copytree_to_existing_destination(os.path.join(base, 'a', 'b', 'c'), os.path.join(base, 'D'))
         with open(os.path.join(base, 'D'), 'r') as file:
             self.assertEqual(file.read(), '3')
+
+    def test_normalize_filename(self):
+        normalize_filename = files.normalize_filename
+
+        self.assertEqual(normalize_filename('~'), normalize_filename('~' + getpass.getuser()))
+        self.assertEqual(normalize_filename('~'), normalize_filename('$HOME'))
+        cur_dir = os.path.dirname(__file__)
+        self.assertEqual(cur_dir,
+            normalize_filename(os.path.join(cur_dir, '..', os.path.basename(cur_dir))))
+        test_filename = os.path.join(cur_dir, 'test_filename')
+        self.assertEqual(test_filename, normalize_filename('test_filename', dir=os.path.dirname(test_filename)))
+        self.assertEqual(os.path.join(os.getcwd(), 'test_filename'), normalize_filename('test_filename'))
+        with self.assertRaisesRegex(ValueError, r"directory '.+' isn't absolute"):
+            normalize_filename('test_filename', dir='~')
+
+    def test_normalize_filenames(self):
+        tmp_path = os.path.join(self.dirname, 'foo')
+        self.assertEqual(files.normalize_filenames([tmp_path]), [tmp_path])
+        file_in_dir = os.path.join('dir_name', 'bar')
+        expected_abs_file_in_dir = os.path.join(self.dirname, file_in_dir)
+        self.assertEqual(files.normalize_filenames([tmp_path, file_in_dir], absolute_file=tmp_path),
+            [tmp_path, expected_abs_file_in_dir])
+
+    def test_remove_silently(self):
+        test_file = os.path.join(self.dirname, 'test_file')
+        Path(test_file).touch()
+        self.assertEqual(files.remove_silently(test_file), None)
+
+        no_such_file = os.path.join(self.dirname, 'no_such_file')
+        self.assertEqual(files.remove_silently(no_such_file), None)
+
+        with self.assertRaises(TypeError):
+            files.remove_silently(12)

wc_utils/util/files.py

@@ -1,13 +1,15 @@
 """ File utils
 
 :Author: Jonathan Karr <karr@mssm.edu>
+:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
 :Date: 2018-05-11
 :Copyright: 2018, Karr Lab
 :License: MIT
 """
 
 import os
 import shutil
+import errno
 
 
 def copytree_to_existing_destination(src, dst):
@@ -35,3 +37,67 @@ def copytree_to_existing_destination(src, dst):
                 shutil.copy2(s, d)
     else:
         shutil.copy2(src, dst)
+
+
+def normalize_filename(filename, dir=None):
+    """ Normalize a filename to its fully expanded, real, absolute path
+
+    Expand `filename` by interpreting a user’s home directory, environment variables, and
+    normalizing its path. If `filename` is not an absolute path and `dir` is provided then
+    return a full path of `filename` in `dir`.
+
+    Args:
+        filename (:obj:`str`): a filename
+        dir (:obj:`str`, optional): a directory that contains `filename`
+
+    Returns:
+        :obj:`str`: `filename`'s fully expanded, absolute path
+
+    Raises:
+        :obj:`ValueError`: if neither `filename` after expansion nor `dir` are absolute
+    """
+    filename = os.path.expanduser(filename)
+    filename = os.path.expandvars(filename)
+    if os.path.isabs(filename):
+        return os.path.normpath(filename)
+    elif dir:
+        # raise exception if dir isn't absolute
+        if not os.path.isabs(dir):
+            raise ValueError("directory '{}' isn't absolute".format(dir))
+        return os.path.normpath(os.path.join(dir, filename))
+    else:
+        return os.path.abspath(filename)
+
+
+def normalize_filenames(filenames, absolute_file=None):
+    """ Normalize filenames relative to directory containing existing file
+
+    Args:
+        filenames (:obj:`list` of :obj:`str`): list of filenames
+        absolute_file (:obj:`str`, optional): file whose directory contains files in `filenames`
+
+    Returns:
+        :obj:`list` of :obj:`str`: absolute paths for files in `filenames`
+    """
+    dir = None
+    if absolute_file:
+        dir = os.path.dirname(absolute_file)
+    return [normalize_filename(filename, dir=dir) for filename in filenames]
+
+
+def remove_silently(filename):
+    """ Delete file `filename` if it exist, but report no error if it doesn't
+
+    Args:
+        filename (:obj:`str`): a filename
+
+    Raises:
+        :obj:`Exception`: if an error occurs that is not 'no such file or directory'
+    """
+    try:
+        os.remove(filename)
+    except OSError as e:
+        # errno.ENOENT: no such file or directory
+        if e.errno != errno.ENOENT:
+            # re-raise exception if a different error occurred
+            raise   # pragma: no cover; unclear how to execute this line