Improve query for fetching a phenotype dataset's data

1 files changed, 8 insertions, 6 deletions

diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index c3b6dfb..d99aa36 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -76,14 +76,16 @@ def phenotypes_data(conn: mdb.Connection,
                     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 "
+    # — Phenotype -> PublishXRef -> PublishData -> Strain -> StrainXRef -> PublishFreeze
+    _query = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode "
+              "FROM Phenotype AS pheno "
+              "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
               "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") + (
+              "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId "
+              "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId "
+              "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId "
+              "WHERE pxr.InbredSetId=%s AND pf.Id=%s") + (
                   f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(_query, (population_id, dataset_id))