Retrieve ALL markers for a species regardless of data.

Retrieve all the genetic markers that exist for a particular species
regardless of whether or not a particular marker has corresponding
samples allele data.

1 files changed, 6 insertions, 7 deletions

diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py
index 4f09b02..34d2cfe 100644
--- a/uploader/genotypes/models.py
+++ b/uploader/genotypes/models.py
@@ -29,29 +29,28 @@ def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int:
 def genotype_markers(
         conn: mdb.Connection,
         species_id: int,
-        dataset_id: int,
         offset: int = 0,
         limit: Optional[int] = None
 ) -> tuple[tuple[dict, ...], int]:
     """Retrieve markers from the database."""
     _query_template = (
-        "SELECT %%COLS%% FROM GenoXRef AS gxr INNER JOIN Geno AS gno "
-        "ON gxr.GenoId=gno.Id WHERE gxr.GenoFreezeId=%s AND gno.SpeciesId=%s "
+        "SELECT %%COLS%% FROM Geno AS gno "
+        "WHERE gno.SpeciesId=%s "
         "%%LIMIT%%")
 
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
             _query_template.replace("%%LIMIT%%", "").replace(
-                "%%COLS%%", "COUNT(gxr.GenoId) AS total_records"),
-            (species_id, dataset_id))
+                "%%COLS%%", "COUNT(gno.Id) AS total_records"),
+            (species_id,))
         _total_records = cursor.fetchone()["total_records"]
         cursor.execute(
-            _query_template.replace("%%COLS%%", "gxr.GenoFreezeId, gno.*").replace(
+            _query_template.replace("%%COLS%%", "gno.*").replace(
                 "%%LIMIT%%",
                 (f"LIMIT {int(limit)} OFFSET {int(offset)}"
                  if bool(limit) and limit > 0
                  else "")),
-            (species_id, dataset_id))
+            (species_id,))
         debug_query(cursor, app.logger)
         return tuple(dict(row) for row in cursor.fetchall()), _total_records