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authorBonfaceKilz2021-06-03 11:08:58 +0300
committerzsloan2021-06-18 22:08:04 +0000
commitc96b29e63577f7189afd02df2ced26b150830341 (patch)
tree21fefb4bd88e9d497965a34e9f9ab4a57600bfd4
parent9d46f943894e15b4a70c64ecba6a3b684863a81f (diff)
downloadgenenetwork3-c96b29e63577f7189afd02df2ced26b150830341.tar.gz
Add data structures for the table metadata_audit
-rw-r--r--gn3/db/__init__.py5
-rw-r--r--gn3/db/metadata_audit.py26
-rw-r--r--tests/unit/db/test_audit.py28
3 files changed, 59 insertions, 0 deletions
diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index d89dbf4..175a640 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -5,21 +5,26 @@ from dataclasses import dataclass, asdict, astuple
from typing_extensions import Protocol
from MySQLdb import escape_string
+from gn3.db.metadata_audit import MetadataAudit
from gn3.db.phenotypes import Phenotype
from gn3.db.phenotypes import PublishXRef
from gn3.db.phenotypes import Publication
+from gn3.db.metadata_audit import metadata_audit_mapping
from gn3.db.phenotypes import phenotype_mapping
from gn3.db.phenotypes import publish_x_ref_mapping
from gn3.db.phenotypes import publication_mapping
+
TABLEMAP = {
+ "metadata_audit": metadata_audit_mapping,
"Phenotype": phenotype_mapping,
"PublishXRef": publish_x_ref_mapping,
"Publication": publication_mapping,
}
DATACLASSMAP = {
+ "MetadataAudit": MetadataAudit,
"Phenotype": Phenotype,
"PublishXRef": PublishXRef,
"Publication": Publication,
diff --git a/gn3/db/metadata_audit.py b/gn3/db/metadata_audit.py
new file mode 100644
index 0000000..6e22b32
--- /dev/null
+++ b/gn3/db/metadata_audit.py
@@ -0,0 +1,26 @@
+# pylint: disable=[R0902, R0903]
+"""This contains all the necessary functions that access the metadata_audit
+table from the db
+
+"""
+from dataclasses import dataclass
+from typing import Optional
+
+
+@dataclass(frozen=True)
+class MetadataAudit:
+ """Data Type that represents a Phenotype"""
+ dataset_id: int
+ editor: str
+ json_data: str
+ time_stamp: Optional[str] = None
+
+
+# Mapping from the MetadataAudit dataclass to the actual column names in the
+# database
+metadata_audit_mapping = {
+ "dataset_id": "dataset_id",
+ "editor": "editor",
+ "json_data": "json_data",
+ "time_stamp": "time_stamp",
+}
diff --git a/tests/unit/db/test_audit.py b/tests/unit/db/test_audit.py
new file mode 100644
index 0000000..22787bb
--- /dev/null
+++ b/tests/unit/db/test_audit.py
@@ -0,0 +1,28 @@
+"""Tests for db/phenotypes.py"""
+import json
+from unittest import TestCase
+from unittest import mock
+
+from gn3.db import insert
+from gn3.db.metadata_audit import MetadataAudit
+
+
+class TestMetadatAudit(TestCase):
+ """Test cases for fetching chromosomes"""
+
+ def test_insert_into_metadata_audit(self):
+ """Test that data is inserted correctly in the audit table
+
+ """
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ type(cursor).rowcount = 1
+ self.assertEqual(insert(
+ conn=db_mock, table="metadata_audit",
+ data=MetadataAudit(dataset_id=35,
+ editor="Bonface",
+ json_data=json.dumps({"a": "b"}))), 1)
+ cursor.execute.assert_called_once_with(
+ "INSERT INTO metadata_audit ('dataset_id', "
+ "'editor', 'json_data') "
+ 'VALUES (\'35\', \'Bonface\', \'{\\"a\\": \\"b\\"}\')')