db: species: Fetch chromosomes using a group or species name

* gn3/db/species.py (get_chromosome): New function.

1 files changed, 24 insertions, 0 deletions

diff --git a/gn3/db/species.py b/gn3/db/species.py
new file mode 100644
index 0000000..91b78e2
--- /dev/null
+++ b/gn3/db/species.py
@@ -0,0 +1,24 @@
+"""This module contains db functions that get data related to species or
+groups. Particularly useful when generating the menu
+
+"""
+from typing import Any, Optional, Tuple
+from MySQLdb import escape_string
+
+
+def get_chromosome(name: str, is_species: bool, conn: Any) -> Optional[Tuple]:
+    """Given either a group or a species Name, return all the species"""
+    _sql = ("SELECT Chr_Length.Name, Chr_Length.OrderId, "
+            "Length FROM Chr_Length, Species WHERE "
+            "Chr_Length.SpeciesId = Species.SpeciesId AND "
+            "Species.Name = "
+            f"'{escape_string(name).decode('UTF-8')}' ORDER BY OrderId")
+    if not is_species:
+        _sql = ("SELECT Chr_Length.Name, Chr_Length.OrderId, "
+                "Length FROM Chr_Length, InbredSet WHERE "
+                "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
+                "InbredSet.Name = "
+                f"'{escape_string(name).decode('UTF-8')}' ORDER BY OrderId")
+    with conn.cursor() as cursor:
+        cursor.execute(_sql)
+        return cursor.fetchall()