Add new procedure for looking up files in a given ENV variable

* gn3/file_utils.py (lookup_file): New function.
* tests/unit/test_file_utils.py: New test cases for ^^.

2 files changed, 46 insertions, 0 deletions

diff --git a/gn3/file_utils.py b/gn3/file_utils.py
index 8e342c9..36e3b6d 100644
--- a/gn3/file_utils.py
+++ b/gn3/file_utils.py
@@ -18,3 +18,19 @@ def get_dir_hash(directory: str) -> str:
                     md5hash.update(bytearray(hashlib.md5(buf).hexdigest(),
                                              "utf-8"))
     return md5hash.hexdigest()
+
+
+def lookup_file(environ_var: str,
+                root_dir: str,
+                file_name: str) -> str:
+    """Look up FILE_NAME in the path defined by ENVIRON_VAR/ROOT_DIR/; If
+ENVIRON_VAR/ROOT_DIR/FILE_NAME does not exist, raise an exception.
+Otherwise return ENVIRON_VAR/ROOT_DIR/FILE_NAME.
+
+    """
+    _dir = os.environ.get(environ_var)
+    if _dir:
+        _file = os.path.join(_dir, root_dir, file_name)
+        if os.path.isfile(_file):
+            return _file
+    raise FileNotFoundError
diff --git a/tests/unit/test_file_utils.py b/tests/unit/test_file_utils.py
index e6109bb..231dcd0 100644
--- a/tests/unit/test_file_utils.py
+++ b/tests/unit/test_file_utils.py
@@ -2,6 +2,8 @@
 import os
 import unittest
 
+from unittest import mock
+from gn3.file_utils import lookup_file
 from gn3.file_utils import get_dir_hash
 
 
@@ -18,3 +20,31 @@ class TestFileUtils(unittest.TestCase):
         self.assertRaises(FileNotFoundError,
                           get_dir_hash,
                           "/non-existent-file")
+
+    @mock.patch("os.path.isfile")
+    @mock.patch.dict(os.environ, {"GENENETWORK_FILES": "/tmp/"})
+    def test_lookup_genotype_file_exists(self, mock_isfile):
+        """Test whether genotype file exists if file is present"""
+        mock_isfile.return_value = True
+        self.assertEqual(lookup_file("GENENETWORK_FILES",
+                                     "genotype_files", "genotype.txt"),
+                         "/tmp/genotype_files/genotype.txt")
+
+    @mock.patch("os.path.isfile")
+    @mock.patch.dict(os.environ, {"GENENETWORK_FILES": "/tmp"})
+    def test_lookup_genotype_file_does_not_exist(self, mock_isfile):
+        """Test whether genotype file exists if file is absent"""
+        mock_isfile.return_value = False
+        self.assertRaises(FileNotFoundError,
+                          lookup_file,
+                          "GENENETWORK_FILES",
+                          "genotype_files",
+                          "genotype.txt")
+
+    def test_lookup_genotype_file_env_does_not_exist(self):
+        """Test whether genotype file exists if GENENETWORK_FILES is absent"""
+        self.assertRaises(FileNotFoundError,
+                          lookup_file,
+                          "GENENETWORK_FILES",
+                          "genotype_files",
+                          "genotype.txt")