Extract common database functions into a separate package.

5 files changed, 80 insertions, 62 deletions

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()
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 2282c8d..881c913 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -5,7 +5,6 @@ from typing import Union
 from functools import reduce
 from datetime import datetime
 
-import MySQLdb as mdb
 from redis import Redis
 from MySQLdb.cursors import DictCursor
 from flask import (
@@ -31,28 +30,6 @@ def make_menu_items_grouper(grouping_fn=lambda item: item):
         return {**acc, grouping: (acc[grouping] + (row_values,))}
     return __grouper__
 
-def species() -> tuple:
-    "Retrieve the species from the database."
-    with database_connection() as conn:
-        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) -> Union[dict, None]:
-    "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()
-
 def genechips():
     "Retrieve the genechip information from the database"
     def __organise_by_species__(acc, chip):
@@ -94,16 +71,6 @@ def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
 
     return tuple()
 
-def groups_by_species(speciesid:int) -> tuple:
-    "Retrieve group (InbredSet) information from the database."
-    with database_connection() as conn:
-        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 organise_groups_by_family(acc:dict, group:dict) -> dict:
     "Organise the group (InbredSet) information by the group field"
     family = group["Family"]
diff --git a/qc_app/samples.py b/qc_app/samples.py
index d27164e..107e889 100644
--- a/qc_app/samples.py
+++ b/qc_app/samples.py
@@ -48,35 +48,6 @@ def select_species():
     flash("You need to select a species", "alert-error")
     return index_page
 
-def save_population(conn: mdb.Connection, population_details: dict) -> int:
-    """Save the population details to the db."""
-    with conn.cursor(cursorclass=DictCursor) 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 new_id
-
-def population_by_id(conn: mdb.Connection, population_id: int) -> 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()
-
 @samples.route("/upload/create-population", methods=["POST"])
 def create_population():
     """Create new grouping/population."""