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-rw-r--r--gn3/db/case_attributes.py132
-rw-r--r--gn3/db/sample_data.py10
-rw-r--r--tests/unit/db/test_case_attributes.py205
3 files changed, 338 insertions, 9 deletions
diff --git a/gn3/db/case_attributes.py b/gn3/db/case_attributes.py
new file mode 100644
index 0000000..8eb2bf6
--- /dev/null
+++ b/gn3/db/case_attributes.py
@@ -0,0 +1,132 @@
+"""Module that contains functions for editing case-attribute data"""
+from typing import Any, Optional, Tuple
+
+import json
+import MySQLdb
+
+
+def get_case_attributes(conn) -> Optional[Tuple]:
+ """Get all the case attributes from the database."""
+ with conn.cursor() as cursor:
+ cursor.execute("SELECT Id, Name, Description FROM CaseAttribute")
+ return cursor.fetchall()
+
+
+def get_unreviewed_diffs(conn: Any) -> Optional[tuple]:
+ """Fetch all case attributes in GN"""
+ with conn.cursor() as cursor:
+ cursor.execute(
+ "SELECT id, editor, json_diff_data FROM "
+ "caseattributes_audit WHERE status = 'review'"
+ )
+ return cursor.fetchall()
+
+
+def insert_case_attribute_audit(
+ conn: Any, status: str, author: str, data: str
+) -> int:
+ """Update the case_attribute_audit table"""
+ rowcount = 0
+ try:
+ with conn.cursor() as cursor:
+ cursor.execute(
+ "INSERT INTO caseattributes_audit "
+ "(status, editor, json_diff_data) "
+ "VALUES (%s, %s, %s)",
+ (status, author, data),
+ )
+ rowcount = cursor.rowcount
+ conn.commit()
+ except Exception as _e:
+ conn.rollback()
+ raise MySQLdb.Error(_e) from _e
+ return rowcount
+
+
+def reject_case_attribute(conn: Any, case_attr_audit_id: int) -> int:
+ """Given the id of the json_diff in the case_attribute_audit table, reject
+ it"""
+ rowcount = 0
+ try:
+ with conn.cursor() as cursor:
+ cursor.execute(
+ "UPDATE caseattributes_audit SET "
+ "status = 'rejected' WHERE id = %s",
+ (case_attr_audit_id,),
+ )
+ rowcount = cursor.rowcount
+ conn.commit()
+ except Exception as _e:
+ conn.rollback()
+ raise MySQLdb.Error(_e) from _e
+ return rowcount
+
+
+def approve_case_attribute(conn: Any, case_attr_audit_id: int) -> int:
+ """Given the id of the json_diff in the case_attribute_audit table,
+ approve it
+
+ """
+ rowcount = 0
+ try:
+ with conn.cursor() as cursor:
+ cursor.execute(
+ "SELECT json_diff_data FROM caseattributes_audit "
+ "WHERE id = %s",
+ (case_attr_audit_id,),
+ )
+ diff_data = cursor.fetchone()
+ if diff_data:
+ diff_data = json.loads(diff_data[0])
+ # Insert (Most Important)
+ if diff_data.get("Insert"):
+ data = diff_data.get("Insert")
+ cursor.execute(
+ "INSERT INTO CaseAttribute "
+ "(Name, Description) VALUES "
+ "(%s, %s)",
+ (
+ data.get("name").strip(),
+ data.get("description").strip(),
+ ),
+ )
+ # Delete
+ elif diff_data.get("Deletion"):
+ data = diff_data.get("Deletion")
+ cursor.execute(
+ "DELETE FROM CaseAttribute " "WHERE Id = %s",
+ (data.get("id"),),
+ )
+ # Modification
+ elif diff_data.get("Modification"):
+ data = diff_data.get("Modification")
+ if desc_ := data.get("description"):
+ cursor.execute(
+ "UPDATE CaseAttribute SET "
+ "Description = %s WHERE Id = %s",
+ (
+ desc_.get("Current"),
+ diff_data.get("id"),
+ ),
+ )
+ if name_ := data.get("name"):
+ cursor.execute(
+ "UPDATE CaseAttribute SET "
+ "Name = %s WHERE Id = %s",
+ (
+ name_.get("Current"),
+ diff_data.get("id"),
+ ),
+ )
+ if cursor.rowcount:
+ cursor.execute(
+ "UPDATE caseattributes_audit SET "
+ "status = 'approved' WHERE id = %s",
+ (case_attr_audit_id,),
+ )
+ rowcount = cursor.rowcount
+ conn.commit()
+ except Exception as _e:
+ conn.rollback()
+ raise MySQLdb.Error(_e) from _e
+ return rowcount
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index f79ce97..d29f6c8 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -1,8 +1,7 @@
"""Module containing functions that work with sample data"""
-from typing import Any, Tuple, Dict, Callable, Optional
+from typing import Any, Tuple, Dict, Callable
import re
-import collections
import MySQLdb
from gn3.csvcmp import extract_strain_name
@@ -423,10 +422,3 @@ def insert_sample_data(
except Exception as _e:
conn.rollback()
raise MySQLdb.Error(_e) from _e
-
-
-def get_case_attributes(conn) -> Optional[Tuple]:
- """Get all the case attributes from the database."""
- with conn.cursor() as cursor:
- cursor.execute("SELECT Id, Name, Description FROM CaseAttribute")
- return cursor.fetchall()
diff --git a/tests/unit/db/test_case_attributes.py b/tests/unit/db/test_case_attributes.py
new file mode 100644
index 0000000..175249b
--- /dev/null
+++ b/tests/unit/db/test_case_attributes.py
@@ -0,0 +1,205 @@
+"""Test cases for gn3.db.case_attributes.py"""
+
+import pytest
+from pytest_mock import MockFixture
+from gn3.db.case_attributes import get_unreviewed_diffs
+from gn3.db.case_attributes import get_case_attributes
+from gn3.db.case_attributes import insert_case_attribute_audit
+from gn3.db.case_attributes import approve_case_attribute
+from gn3.db.case_attributes import reject_case_attribute
+
+
+@pytest.mark.unit_test
+def test_get_case_attributes(mocker: MockFixture) -> None:
+ """Test that all the case attributes are fetched correctly"""
+ 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 == (
+ (1, "Condition", None),
+ (2, "Tissue", None),
+ (3, "Age", "Cum sociis natoque penatibus et magnis dis"),
+ (4, "Condition", "Description A"),
+ (5, "Condition", "Description B"),
+ )
+
+
+@pytest.mark.unit_test
+def test_get_unreviewed_diffs(mocker: MockFixture) -> None:
+ """Test that the correct query is called when fetching unreviewed
+ case-attributes diff"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ _ = get_unreviewed_diffs(mock_conn)
+ cursor.fetchall.return_value = ((1, "editor", "diff_data_1"),)
+ cursor.execute.assert_called_once_with(
+ "SELECT id, editor, json_diff_data FROM "
+ "caseattributes_audit WHERE status = 'review'"
+ )
+
+
+@pytest.mark.unit_test
+def test_insert_case_attribute_audit(mocker: MockFixture) -> None:
+ """Test that the updating case attributes uses the correct query"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ _ = insert_case_attribute_audit(
+ mock_conn, status="review", author="Author", data="diff_data"
+ )
+ cursor.execute.assert_called_once_with(
+ "INSERT INTO caseattributes_audit "
+ "(status, editor, json_diff_data) "
+ "VALUES (%s, %s, %s)",
+ ("review", "Author", "diff_data"),
+ )
+
+
+@pytest.mark.unit_test
+def test_reject_case_attribute(mocker: MockFixture) -> None:
+ """Test rejecting a case-attribute"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ _ = reject_case_attribute(
+ mock_conn,
+ case_attr_audit_id=1,
+ )
+ cursor.execute.assert_called_once_with(
+ "UPDATE caseattributes_audit SET "
+ "status = 'rejected' WHERE id = %s",
+ (1,),
+ )
+
+
+@pytest.mark.unit_test
+def test_approve_inserting_case_attribute(mocker: MockFixture) -> None:
+ """Test approving inserting a case-attribute"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ type(cursor).rowcount = 1
+ cursor.fetchone.return_value = (
+ """
+ {"Insert": {"name": "test", "description": "Random Description"}}
+ """,
+ )
+ _ = approve_case_attribute(
+ mock_conn,
+ case_attr_audit_id=3,
+ )
+ calls = [
+ mocker.call(
+ "SELECT json_diff_data FROM caseattributes_audit "
+ "WHERE id = %s",
+ (3,),
+ ),
+ mocker.call(
+ "INSERT INTO CaseAttribute "
+ "(Name, Description) VALUES "
+ "(%s, %s)",
+ (
+ "test",
+ "Random Description",
+ ),
+ ),
+ mocker.call(
+ "UPDATE caseattributes_audit SET "
+ "status = 'approved' WHERE id = %s",
+ (3,),
+ ),
+ ]
+ cursor.execute.assert_has_calls(calls, any_order=False)
+
+
+@pytest.mark.unit_test
+def test_approve_deleting_case_attribute(mocker: MockFixture) -> None:
+ """Test deleting a case-attribute"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ type(cursor).rowcount = 1
+ cursor.fetchone.return_value = (
+ """
+ {"Deletion": {"id": "12", "name": "test", "description": ""}}
+ """,
+ )
+ _ = approve_case_attribute(
+ mock_conn,
+ case_attr_audit_id=3,
+ )
+ calls = [
+ mocker.call(
+ "SELECT json_diff_data FROM caseattributes_audit "
+ "WHERE id = %s",
+ (3,),
+ ),
+ mocker.call("DELETE FROM CaseAttribute " "WHERE Id = %s", ("12",)),
+ mocker.call(
+ "UPDATE caseattributes_audit SET "
+ "status = 'approved' WHERE id = %s",
+ (3,),
+ ),
+ ]
+ cursor.execute.assert_has_calls(calls, any_order=False)
+
+
+@pytest.mark.unit_test
+def test_approve_modifying_case_attribute(mocker: MockFixture) -> None:
+ """Test modifying a case-attribute"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ type(cursor).rowcount = 1
+ cursor.fetchone.return_value = (
+ """
+{
+ "id": "12",
+ "Modification": {
+ "description": {
+ "Current": "Test",
+ "Original": "A"
+ },
+ "name": {
+ "Current": "Height (A)",
+ "Original": "Height"
+ }
+ }
+}""",
+ )
+ _ = approve_case_attribute(
+ mock_conn,
+ case_attr_audit_id=3,
+ )
+ calls = [
+ mocker.call(
+ "SELECT json_diff_data FROM caseattributes_audit "
+ "WHERE id = %s",
+ (3,),
+ ),
+ mocker.call(
+ "UPDATE CaseAttribute SET " "Description = %s WHERE Id = %s",
+ (
+ "Test",
+ "12",
+ ),
+ ),
+ mocker.call(
+ "UPDATE CaseAttribute SET " "Name = %s WHERE Id = %s",
+ (
+ "Height (A)",
+ "12",
+ ),
+ ),
+ mocker.call(
+ "UPDATE caseattributes_audit SET "
+ "status = 'approved' WHERE id = %s",
+ (3,),
+ ),
+ ]
+ cursor.execute.assert_has_calls(calls, any_order=False)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 00:43:54 +0000