added extra method to convert credential json with no quotes

Author: JoshuaHarris391

src/gen3_metadata/gen3_metadata_parser.py

@@ -2,6 +2,7 @@
 import requests
 import pandas as pd
 import jwt
+import re
 
 
 class Gen3MetadataParser:
@@ -20,6 +21,20 @@ def __init__(self, key_file_path):
         self.headers = {}
         self.data_store = {}
         self.data_store_pd = {}
+    
+    def _add_quotes_to_json(self, input_str):
+        try:
+            # Try parsing as-is
+            return json.loads(input_str)
+        except json.JSONDecodeError:
+            # Add quotes around keys
+            fixed = re.sub(r'([{,]\s*)(\w+)\s*:', r'\1"\2":', input_str)
+            # Add quotes around simple string values (skip existing quoted values)
+            fixed = re.sub(r':\s*([A-Za-z0-9._:@/-]+)(?=\s*[},])', r': "\1"', fixed)
+            try:
+                return json.loads(fixed)
+            except json.JSONDecodeError as e:
+                raise ValueError(f"Could not fix JSON: {e}")
 
     def _load_api_key(self) -> dict:
         """
@@ -28,8 +43,27 @@ def _load_api_key(self) -> dict:
         Returns:
             dict: The API key loaded from the JSON file.
         """
-        with open(self.key_file_path) as json_file:
-            return json.load(json_file)
+        try:
+            # Read the file as plain text
+            with open(self.key_file_path, "r") as f:
+                content = f.read()
+            # If the content does not contain any double or single quotes, try to fix it
+            if '"' not in content and "'" not in content:
+                return self._add_quotes_to_json(content)
+
+            # Read the file as JSON
+            with open(self.key_file_path) as json_file:
+                return json.load(json_file)
+        except FileNotFoundError as fnf_err:
+            print(f"File not found: {fnf_err}")
+            raise
+        except json.JSONDecodeError as json_err:
+            print(f"JSON decode error: {json_err}")
+            print("Please make sure the file contains valid JSON with quotes and proper formatting.")
+            raise
+        except Exception as err:
+            print(f"An unexpected error occurred while loading API key: {err}")
+            raise
 
     def _url_from_jwt(self, cred: dict) -> str:
         """

tests/test_gen3_metadata_parser.py

@@ -9,27 +9,89 @@
 
 @pytest.fixture
 def fake_api_key():
-    """Fixture to provide a fake API key. Note: these credentials have been inactivated"""
+    """Fixture to provide a fake API key. Note: these credentials have been inactivated."""
+    # This is a valid JWT and UUID, but is not active.
     return {
-        "api_key": "eyJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV9rZXkiLCJ0eXAiOiJKV1QifQ.eyJwdXIiOiJhcGlfa2V5Iiwic3ViIjoiMjEiLCJpc3MiOiJodHRwczovL2RhdGEudGVzdC5iaW9jb21tb25zLm9yZy5hdS91c2VyIiwiYXVkIjpbImh0dHBzOi8vZGF0YS50ZXN0LmJpb2NvbW1vbnMub3JnLmF1L3VzZXIiXSwiaWF0IjoxNzQyMjUzNDgwLCJleHAiOjE3NDQ4NDU0ODAsImp0aSI6ImI5MDQyNzAxLWIwOGYtNDBkYS04OWEzLTc1M2JlNGVkMTIyOSIsImF6cCI6IiIsInNjb3BlIjpbImdvb2dsZV9jcmVkZW50aWFscyIsIm9wZW5pZCIsImdvb2dsZV9zZXJ2aWNlX2FjY291bnQiLCJkYXRhIiwiZmVuY2UiLCJnb29nbGVfbGluayIsImFkbWluIiwidXNlciIsImdhNGdoX3Bhc3Nwb3J0X3YxIl19.SGPjs6ljCJbwDu-6WAnI5dN8o5467_ktcnsxRFrX_aCQNrOwSPgTCDvWEzamRmB5Oa0yB6cnjduhWRKnPWIZDal86H0etm77wilCteHF_zFl1IV6LW23AfOVOG3zB9KL6o-ZYqpSRyo0FDj0vQJzrHXPjqvQ15S6Js2sIwIa3ONTeHbR6fRecfPaLK1uGIY5tJFeigXzrLzlifKCEnt_2gqpMU2_b2QgW1315FixNIUOl8A7FZJ2-ddSMJPO0IYQ0QMSWV9-bbxie4Zjsaa1HtQYOhfXLU3vSdUOBO0btSfd6-NnWfx_-lDo5V9lkSH_aecEyew0IHBx-e7rSR5cxA",
+        "api_key": (
+            "eyJhbGciOiJSUzI1NiIsImtpZCI6ImZlbmNlX2tleV9rZXkiLCJ0eXAiOiJKV1QifQ."
+            "eyJwdXIiOiJhcGlfa2V5Iiwic3ViIjoiMjEiLCJpc3MiOiJodHRwczovL2RhdGEudGVzdC5i"
+            "aW9jb21tb25zLm9yZy5hdS91c2VyIiwiYXVkIjpbImh0dHBzOi8vZGF0YS50ZXN0LmJpb2Nv"
+            "bW1vbnMub3JnLmF1L3VzZXIiXSwiaWF0IjoxNzQyMjUzNDgwLCJleHAiOjE3NDQ4NDU0ODAs"
+            "Imp0aSI6ImI5MDQyNzAxLWIwOGYtNDBkYS04OWEzLTc1M2JlNGVkMTIyOSIsImF6cCI6IiIs"
+            "InNjb3BlIjpbImdvb2dsZV9jcmVkZW50aWFscyIsIm9wZW5pZCIsImdvb2dsZV9zZXJ2aWNl"
+            "X2FjY291bnQiLCJkYXRhIiwiZmVuY2UiLCJnb29nbGVfbGluayIsImFkbWluIiwidXNlciIs"
+            "ImdhNGdoX3Bhc3Nwb3J0X3YxIl19."
+            "SGPjs6ljCJbwDu-6WAnI5dN8o5467_ktcnsxRFrX_aCQNrOwSPgTCDvWEzamRmB5Oa0yB6cn"
+            "jduhWRKnPWIZDal86H0etm77wilCteHF_zFl1IV6LW23AfOVOG3zB9KL6o-ZYqpSRyo0FDj0"
+            "vQJzrHXPjqvQ15S6Js2sIwIa3ONTeHbR6fRecfPaLK1uGIY5tJFeigXzrLzlifKCEnt_2gqp"
+            "MU2_b2QgW1315FixNIUOl8A7FZJ2-ddSMJPO0IYQ0QMSWV9-bbxie4Zjsaa1HtQYOhfXLU3v"
+            "SdUOBO0btSfd6-NnWfx_-lDo5V9lkSH_aecEyew0IHBx-e7rSR5cxA"
+        ),
         "key_id": "b9042701-b08f-40da-89a3-753be4ed1229"
     }
 
 @pytest.fixture
 def gen3_metadata_parser():
     """Fixture to create a Gen3MetadataParser instance."""
-    return Gen3MetadataParser(
-        key_file_path="fake_credentials.json"
-    )
+    return Gen3MetadataParser(key_file_path="fake_credentials.json")
 
+@pytest.fixture
+def malformed_json_credentials():
+    """Fixture for malformed JSON credentials (no quotes, not valid Python dict)."""
+    # This is a string, not a dict, to simulate malformed file content.
+    return '{api_key: abc.def.ghi, key_id: 18bdaa-b018}'
+
+def test_add_quotes_to_json_valid(gen3_metadata_parser):
+    """Test _add_quotes_to_json with valid JSON (should parse as-is)."""
+    valid_json = '{"api_key": "abc.def.ghi", "key_id": "18bdaa-b018"}'
+    result = gen3_metadata_parser._add_quotes_to_json(valid_json)
+    assert result == {"api_key": "abc.def.ghi", "key_id": "18bdaa-b018"}
+
+def test_add_quotes_to_json_malformed(gen3_metadata_parser):
+    """Test _add_quotes_to_json with malformed JSON (no quotes)."""
+    malformed = '{api_key: abc.def.ghi, key_id: 18bdaa-b018}'
+    result = gen3_metadata_parser._add_quotes_to_json(malformed)
+    assert result == {"api_key": "abc.def.ghi", "key_id": "18bdaa-b018"}
+
+def test_add_quotes_to_json_url_and_uuid(gen3_metadata_parser):
+    """Test _add_quotes_to_json with keys/values including url and uuid."""
+    malformed = '{key1: value1, key2:123, url: https://example.com, uuid: 18bdaa-b018}'
+    result = gen3_metadata_parser._add_quotes_to_json(malformed)
+    assert result == {
+        "key1": "value1",
+        "key2": "123",
+        "url": "https://example.com",
+        "uuid": "18bdaa-b018"
+    }
+
+def test_add_quotes_to_json_invalid(gen3_metadata_parser):
+    """Test _add_quotes_to_json with unrecoverable malformed JSON."""
+    bad = '{key1 value1, key2:}'
+    with pytest.raises(ValueError):
+        gen3_metadata_parser._add_quotes_to_json(bad)
 
-def test_load_api_key(gen3_metadata_parser, fake_api_key):
-    """Test the _load_api_key method."""
-    # Mock open() to simulate reading the fake API key from a file
+def test_load_api_key_valid_json(gen3_metadata_parser, fake_api_key):
+    """Test the _load_api_key method with valid JSON file content."""
+    # Simulate reading a valid JSON file
     with patch("builtins.open", mock_open(read_data=json.dumps(fake_api_key))):
         result = gen3_metadata_parser._load_api_key()
         assert result == fake_api_key
 
+def test_load_api_key_malformed_json(gen3_metadata_parser, malformed_json_credentials):
+    """Test the _load_api_key method with malformed JSON (no quotes)."""
+    # Simulate reading a malformed JSON file (no quotes)
+    with patch("builtins.open", mock_open(read_data=malformed_json_credentials)):
+        result = gen3_metadata_parser._load_api_key()
+        assert result == {"api_key": "abc.def.ghi", "key_id": "18bdaa-b018"}
+
+def test_load_api_key_invalid_json(gen3_metadata_parser):
+    """Test the _load_api_key method with unrecoverable malformed JSON."""
+    # Simulate reading a badly malformed JSON file
+    bad_content = '{key1 value1, key2:}'
+    with patch("builtins.open", mock_open(read_data=bad_content)):
+        with pytest.raises(ValueError):
+            gen3_metadata_parser._load_api_key()
+
 def test_url_from_jwt(gen3_metadata_parser, fake_api_key):
     """Test if you can infer the data commons url from the JWT token"""
     url = gen3_metadata_parser._url_from_jwt(fake_api_key)