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authorFrederick Muriuki Muriithi2024-01-08 04:50:42 +0300
committerFrederick Muriuki Muriithi2024-01-08 05:46:25 +0300
commitcace7a50a45c6d227bce52569fcfc2944fbcbe92 (patch)
treebf625ff1467ba808784fa00c0852c35cd9f1d6ce /qc_app/db
parent0677b36b2e144b07d7822661129cde0a82115b12 (diff)
downloadgn-uploader-cace7a50a45c6d227bce52569fcfc2944fbcbe92.tar.gz
Extract common database functions into a separate package.
Diffstat (limited to 'qc_app/db')
-rw-r--r--qc_app/db/__init__.py7
-rw-r--r--qc_app/db/populations.py49
-rw-r--r--qc_app/db/species.py24
3 files changed, 80 insertions, 0 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()