Extract common database functions into a separate package.

1 files changed, 49 insertions, 0 deletions

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}