1 files changed, 102 insertions, 0 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
new file mode 100644
index 0000000..4c3e634
--- /dev/null
+++ b/uploader/genotypes/models.py
@@ -0,0 +1,102 @@
+"""Functions for handling genotypes."""
+from typing import Optional
+from datetime import datetime
+
+import MySQLdb as mdb
+from MySQLdb.cursors import Cursor, DictCursor
+from flask import current_app as app
+
+from gn_libs.mysqldb 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:# type: ignore[operator]
+        _query = _query + f" LIMIT {limit} OFFSET {offset}"
+
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(_query, (species_id,))
+        debug_query(cursor, app.logger)
+        return tuple(dict(row) for row in cursor.fetchall())
+
+
+def genotype_dataset(
+        conn: mdb.Connection,
+        species_id: int,
+        population_id: int,
+        dataset_id: Optional[int] = None
+) -> Optional[dict]:
+    """Retrieve genotype datasets from the database.
+
+    Apparently, you should only ever have one genotype dataset for a population.
+    """
+    _query = (
+        "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset "
+        "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf "
+        "ON iset.Id=gf.InbredSetId "
+        "WHERE s.Id=%s AND iset.Id=%s")
+    _params = (species_id, population_id)
+    if bool(dataset_id):
+        _query = _query + " AND gf.Id=%s"
+        _params = _params + (dataset_id,)# type: ignore[assignment]
+
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(_query, _params)
+        debug_query(cursor, app.logger)
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+        return None
+
+
+def save_new_dataset(
+        cursor: Cursor,
+        population_id: int,
+        name: str,
+        fullname: str,
+        shortname: str
+) -> dict:
+    """Save a new genotype dataset into the database."""
+    params = {
+        "InbredSetId": population_id,
+        "Name": name,
+        "FullName": fullname,
+        "ShortName": shortname,
+        "CreateTime": datetime.now().date().isoformat(),
+        "public": 2,
+        "confidentiality": 0,
+        "AuthorisedUsers": None
+    }
+    cursor.execute(
+        "INSERT INTO GenoFreeze("
+        "Name, FullName, ShortName, CreateTime, public, InbredSetId, "
+        "confidentiality, AuthorisedUsers"
+        ") VALUES ("
+        "%(Name)s, %(FullName)s, %(ShortName)s, %(CreateTime)s, %(public)s, "
+        "%(InbredSetId)s, %(confidentiality)s, %(AuthorisedUsers)s"
+        ")",
+        params)
+    return {**params, "Id": cursor.lastrowid}