Start building up the view dataset endpoint

1 files changed, 31 insertions, 0 deletions

diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 1f72dbd..4ef674f 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -20,3 +20,34 @@ def datasets_by_population(
             "WHERE s.Id=%s AND iset.Id=%s;",
                        (species_id, population_id))
         return tuple(dict(row) for row in cursor.fetchall())
+
+
+def phenotypes_data(conn: mdb.Connection,
+                    population_id: int,
+                    dataset_id: int,
+                    offset: int = 0,
+                    limit: Optional[int] = None) -> tuple[dict, ...]:
+    """Fetch the data for the phenotypes."""
+    #TODO: This query isn't exactly right, it misses some data.
+    # — Phenotype -> PublishXRef -> PublishData -> Strain -> PublishFreeze
+    _query = ("SELECT pxr.*, pd.*, str.* FROM PublishFreeze AS pf "
+              "INNER JOIN PublishXRef AS pxr ON pf.InbredSetId=pxr.InbredSetId "
+              "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id "
+              "INNER JOIN Strain AS str ON pd.StrainId=str.Id "
+              "WHERE pf.InbredSetId=%s AND pf.Id=%s "
+              "ORDER BY pxr.DataId ASC, str.Id ASC") + (
+                  f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(_query, (population_id, dataset_id))
+        debug_query(cursor)
+        return tuple(dict(row) for row in cursor.fetchall())
+
+
+def phenotypes_se(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]:
+    """Fetch the standard errors for the phenotypes."""
+    return tuple()
+
+
+def phenotypes_sample_counts(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]:
+    """Fetch the standard errors for the phenotypes."""
+    return tuple()