From 6ca2c1520b1fc6e1472fbc74994e3e136cacdc71 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 30 Sep 2024 16:54:28 -0500
Subject: BugFix: Ensure all data items show up.

---
 uploader/phenotypes/models.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

(limited to 'uploader/phenotypes')

diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index eb5a189..be970ac 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -78,7 +78,7 @@ def __phenotype_se__(cursor: Cursor,
                      xref_id: str) -> dict:
     """Fetch standard-error values (if they exist) for a phenotype."""
     _sequery = (
-        "SELECT pxr.Id AS xref_id, pxr.DataId, pse.error, nst.count "
+        "SELECT pxr.Id AS xref_id, pxr.DataId, str.Id AS StrainId, pse.error, nst.count "
         "FROM Phenotype AS pheno "
         "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
         "INNER JOIN PublishSE AS pse ON pxr.DataId=pse.DataId "
@@ -90,7 +90,12 @@ def __phenotype_se__(cursor: Cursor,
         "WHERE (str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)")
     cursor.execute(_sequery,
                    (species_id, population_id, dataset_id, xref_id))
-    return {row["xref_id"]: dict(row) for row in cursor.fetchall()}
+    return {(row["DataId"], row["StrainId"]): {
+        "xref_id": row["xref_id"],
+        "DataId": row["DataId"],
+        "error": row["error"],
+        "count": row["count"]
+    } for row in cursor.fetchall()}
 
 def __organise_by_phenotype__(pheno, row):
     """Organise disparate data rows into phenotype 'objects'."""
@@ -105,11 +110,10 @@ def __organise_by_phenotype__(pheno, row):
             "Units": row["Units"],
             "Pre_publication_abbreviation": row["Pre_publication_abbreviation"],
             "Post_publication_abbreviation": row["Post_publication_abbreviation"],
+            "xref_id": row["pxr.Id"],
             "data": {
-                #TOD0: organise these by DataId and StrainId
                 **(_pheno["data"] if bool(_pheno) else {}),
-                row["pxr.Id"]: {
-                    "xref_id": row["pxr.Id"],
+                (row["DataId"], row["StrainId"]): {
                     "DataId": row["DataId"],
                     "mean": row["mean"],
                     "Locus": row["Locus"],
@@ -168,7 +172,7 @@ def phenotype_by_id(
                                      species_id,
                                      population_id,
                                      dataset_id,
-                                     xref_id)).items())
+                                     xref_id)).values())
             }
         if bool(_pheno) and len(_pheno.keys()) > 1:
             raise Exception(
-- 
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