Add method for updating values from a sample dataset

* gn3/db/traits.py (update_sample_data): New function.
* tests/unit/db/test_traits.py: New test cases for ^^.

3 files changed, 91 insertions, 1 deletions

diff --git a/HACKING.org b/HACKING.org
new file mode 100644
index 0000000..8c26a29
--- /dev/null
+++ b/HACKING.org
@@ -0,0 +1,8 @@
+* Introduction
+
+We are getting away from GitHub CI, and hosting our own CI servers. From GitHub, once a person makes a push, we'll be using [[https://github.com/adnanh/webhook][webhook]] to initiate laminar.
+
+
+First install laminar (use the appropriate binary):
+
+: wget https://github.com/adnanh/webhook/releases/download/2.8.0/webhook-linux-amd64.tar.gz && tar xf webhook-linux-amd64.tar.gz
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 4baac67..a77e6a1 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,5 +1,5 @@
 """This class contains functions relating to trait data manipulation"""
-from typing import Any
+from typing import Any, Union
 
 
 def get_trait_csv_sample_data(conn: Any,
@@ -30,3 +30,48 @@ def get_trait_csv_sample_data(conn: Any,
                           for val in (strain_id, strain_name,
                                       value, error, count)]))
     return f"# Publish Data Id: {publishdata_id}\n\n" + "\n".join(csv_data)
+
+
+def update_sample_data(conn: Any,
+                       strain_name: str,
+                       strain_id: int,
+                       publish_data_id: int,
+                       value: Union[int, float, str],
+                       error: Union[int, float, str],
+                       count: Union[int, str]):
+    """Given the right parameters, update sample-data from the relevant
+    table."""
+    STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s"
+    PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s "
+                             "WHERE StrainId = %s AND Id = %s")
+    PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s "
+                           "WHERE StrainId = %s AND DataId = %s")
+    N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s "
+                         "WHERE StrainId = %s AND DataId = %s")
+
+    updated_strains: int = 0
+    updated_published_data: int = 0
+    updated_se_data: int = 0
+    updated_n_strains: int = 0
+
+    with conn.cursor() as cursor:
+        # Update the Strains table
+        cursor.execute(STRAIN_ID_SQL, (strain_name, strain_id))
+        updated_strains: int = cursor.rowcount
+        # Update the PublishData table
+        cursor.execute(PUBLISH_DATA_SQL,
+                       (None if value == "x" else value,
+                        strain_id, publish_data_id))
+        updated_published_data: int = cursor.rowcount
+        # Update the PublishSE table
+        cursor.execute(PUBLISH_SE_SQL,
+                       (None if error == "x" else error,
+                        strain_id, publish_data_id))
+        updated_se_data: int = cursor.rowcount
+        # Update the NStrain table
+        cursor.execute(N_STRAIN_SQL,
+                       (None if count == "x" else count,
+                        strain_id, publish_data_id))
+        updated_n_strains: int = cursor.rowcount
+    return (updated_strains, updated_published_data,
+            updated_se_data, updated_n_strains)
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
new file mode 100644
index 0000000..0e69bbe
--- /dev/null
+++ b/tests/unit/db/test_traits.py
@@ -0,0 +1,37 @@
+"""Tests for db/traits.py"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.db.traits import update_sample_data
+
+
+class TestTraitsSqlMethods(TestCase):
+    """Test cases for sql operations that affect traits"""
+    def test_update_sample_data(self):
+        """Test that the SQL queries when calling update_sample_data are called with
+        the right calls.
+
+        """
+        db_mock = mock.MagicMock()
+
+        STRAIN_ID_SQL: str = "UPDATE Strain SET Name = '%s' WHERE Id = %s"
+        PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s "
+                                 "WHERE StrainId = %s AND DataId = %s")
+        PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s "
+                               "WHERE StrainId = %s AND DataId = %s")
+        N_STRAIN_SQL: str = ("UPDATE NStrain SET count = '%s' "
+                             "WHERE StrainId = %s AND DataId = %s")
+
+        with db_mock.cursor() as cursor:
+            type(cursor).rowcount = 1
+            self.assertEqual(update_sample_data(
+                conn=db_mock, strain_name="BXD11",
+                strain_id=10, publish_data_id=8967049,
+                value=18.7, error=2.3, count=2),
+                             (1, 1, 1, 1))
+            cursor.execute.assert_has_calls(
+                [mock.call(STRAIN_ID_SQL, ('BXD11', 10)),
+                 mock.call(PUBLISH_DATA_SQL, (18.7, 10, 8967049)),
+                 mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)),
+                 mock.call(N_STRAIN_SQL, (2, 10, 8967049))]
+            )