Display some genotype information.

1 files changed, 41 insertions, 0 deletions

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
new file mode 100644
index 0000000..53c5fb8
--- /dev/null
+++ b/uploader/genotypes/models.py
@@ -0,0 +1,41 @@
+"""Functions for handling genotypes."""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+from uploader.db_utils import debug_query
+
+def genocode_by_population(
+        conn: mdb.Connection, population_id: int) -> tuple[dict, ...]:
+    """Get the allele/genotype codes."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GenoCode WHERE InbredSetId=%s",
+                       (population_id,))
+        return tuple(dict(item) for item in cursor.fetchall())
+
+
+def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int:
+    """Find the total count of the genotype markers for a species."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT COUNT(Name) AS markers_count FROM Geno WHERE SpeciesId=%s",
+            (species_id,))
+        return int(cursor.fetchone()["markers_count"])
+
+
+def genotype_markers(
+        conn: mdb.Connection,
+        species_id: int,
+        offset: int = 0,
+        limit: Optional[int] = None
+) -> tuple[dict, ...]:
+    """Retrieve markers from the database."""
+    _query = "SELECT * FROM Geno WHERE SpeciesId=%s"
+    if bool(limit) and limit > 0:
+        _query = _query + f" LIMIT {limit} OFFSET {offset}"
+
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(_query, (species_id,))
+        debug_query(cursor)
+        return tuple(dict(row) for row in cursor.fetchall())