Add method for fetching the case_attributes

* gn3/db/sample_data.py (get_case_attributes): New function.
* tests/unit/db/test_sample_data.py (test_get_case_attributes): Test case for
the above.

2 files changed, 53 insertions, 0 deletions

diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index 73fbd95..d7ea9d3 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -1,6 +1,7 @@
 """Module containing functions that work with sample data"""
 from typing import Any, Tuple, Dict, Callable
 
+import collections
 import MySQLdb
 
 from gn3.csvcmp import extract_strain_name
@@ -394,3 +395,29 @@ def insert_sample_data(
     except Exception as _e:
         conn.rollback()
         raise MySQLdb.Error(_e) from _e
+
+
+def get_case_attributes(conn) -> dict:
+    """Get all the case attributes as a dictionary from the database. Should there
+    exist more than one case attribute with the same name, put the id in
+    brackets."""
+    results = {}
+    with conn.cursor() as cursor:
+        cursor.execute("SELECT Id, Name, Description FROM CaseAttribute")
+        _r = cursor.fetchall()
+        _dups = [
+            item
+            for item, count in collections.Counter(
+                [name for _, name, _ in _r]
+            ).items()
+            if count > 1
+        ]
+        for _id, _name, _desc in _r:
+            _name = _name.strip()
+            _desc = _desc if _desc else ""
+            if _name in _dups:
+                results[f"{_name} ({_id})"] = _desc
+            else:
+                results[f"{_name}"] = _desc
+
+    return results
diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index 607b278..dad7169 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -4,6 +4,7 @@ import gn3
 
 from gn3.db.sample_data import __extract_actions
 from gn3.db.sample_data import delete_sample_data
+from gn3.db.sample_data import get_case_attributes
 from gn3.db.sample_data import insert_sample_data
 from gn3.db.sample_data import update_sample_data
 
@@ -194,3 +195,28 @@ def test_update_sample_data(mocker):
             ],
             any_order=False,
         )
+
+
+@pytest.mark.unit_test
+def test_get_case_attributes(mocker):
+    """Test that case attributes work well"""
+    mock_conn = mocker.MagicMock()
+    with mock_conn.cursor() as cursor:
+        cursor.fetchall.return_value = (
+            (1, "Condition", None),
+            (2, "Tissue", None),
+            (3, "Age", "Cum sociis natoque penatibus et magnis dis"),
+            (4, "Condition", "Description A"),
+            (5, "Condition", "Description B"),
+        )
+        results = get_case_attributes(mock_conn)
+        cursor.execute.assert_called_once_with(
+            "SELECT Id, Name, Description FROM CaseAttribute"
+        )
+        assert results == {
+            "Condition (1)": "",
+            "Tissue": "",
+            "Age": "Cum sociis natoque penatibus et magnis dis",
+            "Condition (4)": "Description A",
+            "Condition (5)": "Description B",
+        }