Remove the ORM-dependent `update` function.

3 files changed, 49 insertions, 29 deletions

diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
index 9a86ad8..b8c6e20 100644
--- a/gn3/db/__init__.py
+++ b/gn3/db/__init__.py
@@ -43,35 +43,6 @@ class Dataclass(Protocol):
     __dataclass_fields__: Dict
 
 
-def update(conn: Any,
-           table: str,
-           data: Dataclass,
-           where: Dataclass) -> Optional[int]:
-    """Run an UPDATE on a table"""
-    logger.warning(
-        "DEPRECATION WARNING: The function `%s.update` is deprecated and will "
-        "be removed soon. **DO NOT** use it, and remove all references to it "
-        "from your code.",
-        __name__)
-    if not (any(astuple(data)) and any(astuple(where))):
-        return None
-    data_ = {k: v for k, v in asdict(data).items()
-             if v is not None and k in TABLEMAP[table]}
-    where_ = {k: v for k, v in asdict(where).items()
-              if v is not None and k in TABLEMAP[table]}
-    sql = f"UPDATE {table} SET "
-    sql += ", ".join(f"{TABLEMAP[table].get(k)} "
-                     "= %s" for k in data_.keys())
-    sql += " WHERE "
-    sql += " AND ".join(f"{TABLEMAP[table].get(k)} = "
-                        "%s" for k in where_.keys())
-    with conn.cursor() as cursor:
-        cursor.execute(sql,
-                       tuple(data_.values()) + tuple(where_.values()))
-        conn.commit()
-        return cursor.rowcount
-
-
 def diff_from_dict(old: Dict, new: Dict) -> Dict:
     """Construct a new dict with a specific structure that contains the difference
 between the 2 dicts in the structure:
diff --git a/gn3/db/phenotypes.py b/gn3/db/phenotypes.py
index b42118a..2b16b17 100644
--- a/gn3/db/phenotypes.py
+++ b/gn3/db/phenotypes.py
@@ -157,7 +157,42 @@ def update_publication(conn, data=dict) -> int:
     updatable_cols = ", ".join(f"{publication_mapping[col]}=%({col})s"
                                for col in data
                                if col not in ("id_", "id"))
+    if not bool(updatable_cols):
+        return 0
     with conn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
             f"UPDATE Publication SET {updatable_cols} WHERE Id=%(id_)s", data)
         return cursor.rowcount
+
+def update_phenotype(conn, data:dict) -> int:
+    """Update the `Phenotype` table with the given data."""
+    cols = ", ".join(f"{phenotype_mapping[col]}=%({col})s"
+                     for col in data
+                     if col not in ("id_", "id"))
+    if not bool(cols):
+        return 0
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            f"UPDATE Phenotype SET {cols} WHERE Id=%(id_)s", data)
+        return cursor.rowcount
+
+def update_cross_reference(conn, dataset_id, trait_name, data:dict) -> int:
+    """Update the `PublishXRef` table with data."""
+    cols = ", ".join(f"{publish_x_ref_mapping[col]}=%({col})s"
+                     for col in data
+                     if (col not in ("id_", "id") and
+                         col in publish_x_ref_mapping))
+    if not bool(cols):
+        return 0
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            f"UPDATE PublishXRef SET {cols} WHERE "
+            "Id=%(trait_name)s AND "
+            "InbredSetId="
+            "(SELECT InbredSetId FROM PublishFreeze WHERE Id=%(dataset_id)s)",
+            {
+                "dataset_id": dataset_id,
+                "trait_name": trait_name,
+                **data
+            })
+        return cursor.rowcount
diff --git a/gn3/db/probesets.py b/gn3/db/probesets.py
index 19c6896..57ae452 100644
--- a/gn3/db/probesets.py
+++ b/gn3/db/probesets.py
@@ -75,3 +75,17 @@ def fetch_probeset_metadata_by_name(conn: DBConnection, name: str) -> dict:
                         "WHERE Name = %(name)s"),
                        {"name": name})
         return cursor.fetchone()
+
+def update_probeset(conn, probeset_id, data:dict) -> int:
+    """Update the ProbeSet table with given `data`."""
+    cols = ", ".join(f"{probeset_mapping[col]}=%({col})s"
+                     for col in data
+                     if (col not in ("id_", "id") and
+                         col in probeset_mapping))
+    if not bool(cols):
+        return 0
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            f"UPDATE ProbeSet SET {cols} WHERE Id=%(probeset_id)s",
+            {"probeset_id": probeset_id, **data})
+        return cursor.rowcount