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authorFrederick Muriuki Muriithi2024-07-25 11:07:33 -0500
committerFrederick Muriuki Muriithi2024-07-25 14:34:09 -0500
commit754e8f214b940e05298cb360ed829f5c685d55a5 (patch)
tree62c2c5b601746621f0949b38937ad232f006dee2 /uploader/db/populations.py
parentde9e1b9fe37928b864bea28b408de6c14d04526b (diff)
downloadgn-uploader-754e8f214b940e05298cb360ed829f5c685d55a5.tar.gz
Rename module: qc_app --> uploader
Diffstat (limited to 'uploader/db/populations.py')
-rw-r--r--uploader/db/populations.py54
1 files changed, 54 insertions, 0 deletions
diff --git a/uploader/db/populations.py b/uploader/db/populations.py
new file mode 100644
index 0000000..4485e52
--- /dev/null
+++ b/uploader/db/populations.py
@@ -0,0 +1,54 @@
+"""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(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "INSERT INTO InbredSet("
+ "InbredSetId, InbredSetName, Name, SpeciesId, FullName, "
+ "MenuOrderId, Description"
+ ") "
+ "VALUES ("
+ "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, "
+ "%(FullName)s, %(MenuOrderId)s, %(Description)s"
+ ")",
+ {
+ "MenuOrderId": 0,
+ "InbredSetId": 0,
+ **population_details
+ })
+ new_id = cursor.lastrowid
+ cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s",
+ (new_id, new_id))
+ return {
+ **population_details,
+ "Id": new_id,
+ "InbredSetId": new_id,
+ "population_id": new_id
+ }