checkcheck

Author: rmobmina

api/models/efp_schemas.py

@@ -217,6 +217,17 @@ def _simple_schema(
         if "probeset_nullable" in kwargs:
             overrides.setdefault("data_probeset_id", {})["nullable"] = kwargs.pop("probeset_nullable")
 
+        # Build index list, excluding TEXT columns (can't be indexed in MySQL)
+        index_columns = list(DEFAULT_INDEX)
+        if "data_probeset_id" in overrides and overrides["data_probeset_id"].get("type") == "text":
+            index_columns = [col for col in index_columns if col != "data_probeset_id"]
+        if "data_bot_id" in overrides and overrides["data_bot_id"].get("type") == "text":
+            index_columns = [col for col in index_columns if col != "data_bot_id"]
+
+        # Allow manual index override if specified
+        if "index" not in kwargs:
+            kwargs["index"] = index_columns
+
         return EfpSchemaBuilder._build_schema(
             charset=charset,
             column_overrides=overrides,
@@ -261,13 +272,18 @@ def _schema_with_qa_columns(
         extra_columns = kwargs.pop("extra_columns", [])
         all_extra_cols = qa_cols + extra_columns
 
+        # Build index list - exclude data_probeset_id if it's TEXT type
+        index_columns = ["data_probeset_id"]
+        if kwargs.get("probeset_type") == "text":
+            index_columns = []
+
         return EfpSchemaBuilder._simple_schema(
             species=species,
             sample_regex=sample_regex,
             probeset_len=probeset_len,
             bot_id_len=bot_id_len,
             extra_columns=all_extra_cols,
-            index=["data_probeset_id"],
+            index=index_columns,
             **kwargs,
         )
 

api/services/efp_bootstrap.py

@@ -73,6 +73,11 @@ def _build_table(metadata: MetaData, spec, db_name: str) -> Table:
 
     table = Table(spec["table_name"], metadata, *columns, mysql_charset=spec.get("charset"))
     index_cols = spec.get("index") or []
+    if index_cols:
+        # MySQL cannot index TEXT/BLOB columns without a prefix length.
+        # Filter them out to avoid bootstrap failures when schemas use TEXT.
+        text_cols = {col["name"] for col in spec["columns"] if col.get("type") == "text"}
+        index_cols = [col for col in index_cols if col not in text_cols]
     if index_cols:
         index_name = _make_index_name(db_name, index_cols)
         Index(index_name, *[table.c[col] for col in index_cols])