From cace7a50a45c6d227bce52569fcfc2944fbcbe92 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 8 Jan 2024 04:50:42 +0300
Subject: Extract common database functions into a separate package.

---
 qc_app/db/__init__.py    |  7 +++++++
 qc_app/db/populations.py | 49 ++++++++++++++++++++++++++++++++++++++++++++++++
 qc_app/db/species.py     | 24 ++++++++++++++++++++++++
 3 files changed, 80 insertions(+)
 create mode 100644 qc_app/db/__init__.py
 create mode 100644 qc_app/db/populations.py
 create mode 100644 qc_app/db/species.py

(limited to 'qc_app/db')

diff --git a/qc_app/db/__init__.py b/qc_app/db/__init__.py
new file mode 100644
index 0000000..0b48461
--- /dev/null
+++ b/qc_app/db/__init__.py
@@ -0,0 +1,7 @@
+"""Database functions"""
+from .species import species, species_by_id
+from .populations import (
+    save_population,
+    population_by_id,
+    populations_by_species,
+    population_by_species_and_id)
diff --git a/qc_app/db/populations.py b/qc_app/db/populations.py
new file mode 100644
index 0000000..0bcbe5d
--- /dev/null
+++ b/qc_app/db/populations.py
@@ -0,0 +1,49 @@
+"""Functions for accessing the database relating to species populations."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def population_by_id(conn: mdb.Connection, population_id) -> dict:
+    """Get the grouping/population by id."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s",
+                       (population_id,))
+        return cursor.fetchone()
+
+def population_by_species_and_id(
+        conn: mdb.Connection, species_id, population_id) -> dict:
+    """Retrieve a population by its identifier and species."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM InbredSet WHERE SpeciesId=%s AND Id=%s",
+                       (species_id, population_id))
+        return cursor.fetchone()
+
+def populations_by_species(conn: mdb.Connection, speciesid) -> tuple:
+    "Retrieve group (InbredSet) information from the database."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        query = "SELECT * FROM InbredSet WHERE SpeciesId=%s"
+        cursor.execute(query, (speciesid,))
+        return tuple(cursor.fetchall())
+
+    return tuple()
+
+def save_population(conn: mdb.Connection, population_details: dict) -> dict:
+    """Save the population details to the db."""
+    with conn.cursor() as cursor:
+        cursor.execute("SELECT MAX(Id) AS last_id FROM InbredSet")
+        new_id = cursor.fetchone()["last_id"] + 1
+        cursor.execute(
+            "INSERT INTO InbredSet("
+            "Id, InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
+            "MenuOrderId, Description"
+            ") "
+            "VALUES ("
+            "%(Id)s, %(InbredSetId)s, %(InbredSetName)s, %(Name)s, "
+            "%(SpeciesId)s, %(FullName)s, %(MenuOrderId)s, %(Description)s"
+            ")",
+            {
+                "Id": new_id,
+                "InbredSetId": new_id,
+                "MenuOrderId": 0,
+                **population_details
+            })
+        return {**population_details, "population_id": new_id}
diff --git a/qc_app/db/species.py b/qc_app/db/species.py
new file mode 100644
index 0000000..7006d15
--- /dev/null
+++ b/qc_app/db/species.py
@@ -0,0 +1,24 @@
+"""Database functions for species."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def species(conn: mdb.Connection) -> tuple:
+    "Retrieve the species from the database."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
+            "FROM Species")
+        return tuple(cursor.fetchall())
+
+    return tuple()
+
+def species_by_id(conn: mdb.Connection, speciesid) -> dict:
+    "Retrieve the species from the database by id."
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            (
+                "SELECT "
+                "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
+                "FROM Species WHERE SpeciesId=%s"),
+            (speciesid,))
+        return cursor.fetchone()
-- 
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