From a675d462d2771f9e6c497c2385c985c2a6bb8806 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 18 Mar 2025 13:11:41 -0500
Subject: Enable downloading of dataset's phenotype's data.

---
 uploader/phenotypes/models.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'uploader/phenotypes/models.py')

diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index 98278e5..ce7720c 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -254,3 +254,29 @@ def save_new_dataset(cursor: Cursor,
         params)
     debug_query(cursor, app.logger)
     return {**params, "Id": cursor.lastrowid}
+
+
+def phenotypes_data_by_ids(
+        conn: mdb.Connection,
+        inbred_pheno_xref: dict[str, int]
+) -> tuple[dict, ...]:
+    """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping."""
+    _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref))
+    _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 "
+              "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 "
+              f"WHERE (pxr.InbredSetId, pheno.Id, pxr.Id) IN ({_paramstr}) "
+              "ORDER BY pheno.Id")
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(_query, tuple(item for row in inbred_pheno_xref
+                                     for item in (row["population_id"],
+                                                  row["phenoid"],
+                                                  row["xref_id"])))
+        debug_query(cursor, app.logger)
+        return tuple(
+            reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values())
-- 
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