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-rw-r--r--gn3/file_utils.py23
-rw-r--r--tests/unit/test_file_utils.py29
2 files changed, 8 insertions, 44 deletions
diff --git a/gn3/file_utils.py b/gn3/file_utils.py
index 16b2f94..ca80373 100644
--- a/gn3/file_utils.py
+++ b/gn3/file_utils.py
@@ -27,21 +27,14 @@ def get_dir_hash(directory: str) -> str:
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 = APP_DEFAULTS.get(environ_var,
- 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
+def get_dir_hash(directory: str) -> str:
+ """Return the hash of a DIRECTORY"""
+ if not os.path.exists(directory):
+ raise FileNotFoundError
+ all_files = [os.path.join(root, names)
+ for root, _, files in os.walk(directory)
+ for names in sorted(files)]
+ return get_hash_of_files(all_files)
def jsonfile_to_dict(json_file: str) -> Dict:
diff --git a/tests/unit/test_file_utils.py b/tests/unit/test_file_utils.py
index 7f4d83d..af86ba8 100644
--- a/tests/unit/test_file_utils.py
+++ b/tests/unit/test_file_utils.py
@@ -8,7 +8,6 @@ from unittest import mock
from gn3.file_utils import extract_uploaded_file
from gn3.file_utils import get_dir_hash
from gn3.file_utils import jsonfile_to_dict
-from gn3.file_utils import lookup_file
@dataclass
@@ -32,34 +31,6 @@ class TestFileUtils(unittest.TestCase):
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")
-
def test_jsonfile_to_dict(self):
"""Test that a json file is parsed correctly"""""
json_file = os.path.join(os.path.dirname(__file__),