remove 500 search limit

app/db/queries.py

@@ -83,18 +83,50 @@ async def build_conditions(
 
     return where_clause, query_params
 
-def get_query(columns_to_select: str, where_clause: str) -> str:
-    return f"""
+SORTABLE_COLUMNS = {
+    "accession": "pua.accession",
+    "amino_acids": "pua.amino_acids",
+    "organism": "pua.organism",
+    "curation_status": "pua.curation_status",
+    "predicted_ec": "puace.max_clean_ec_confidence",
+}
+
+DEFAULT_ORDER_BY = "puace.max_clean_ec_confidence DESC, pua.amino_acids ASC, pua.predictions_uniprot_annot_id ASC"
+
+
+def parse_ordering(ordering: str | None) -> str:
+    """Parse an ordering string like '-accession' into a SQL ORDER BY clause.
+
+    Returns the default ordering if ordering is None or invalid.
+    """
+    if not ordering:
+        return DEFAULT_ORDER_BY
+
+    descending = ordering.startswith("-")
+    field = ordering.lstrip("-")
+
+    if field not in SORTABLE_COLUMNS:
+        return DEFAULT_ORDER_BY
+
+    direction = "DESC" if descending else "ASC"
+    col = SORTABLE_COLUMNS[field]
+    return f"{col} {direction}, pua.predictions_uniprot_annot_id ASC"
+
+
+def get_query(columns_to_select: str, where_clause: str, include_order_by: bool = True, ordering: str | None = None) -> str:
+    query = f"""
     SELECT
         {columns_to_select}
     FROM cleandb.predictions_uniprot_annot pua
     INNER JOIN cleandb.predictions_uniprot_annot_clean_ec_mv01 puace
         ON puace.predictions_uniprot_annot_id = pua.predictions_uniprot_annot_id
     LEFT JOIN cleandb.predictions_uniprot_annot_ec_mv01 puae
         ON puae.predictions_uniprot_annot_id = pua.predictions_uniprot_annot_id
-    WHERE {where_clause}
-    ORDER BY puace.max_clean_ec_confidence DESC, pua.amino_acids ASC, pua.predictions_uniprot_annot_id ASC
-    """
+    WHERE {where_clause}"""
+    if include_order_by:
+        query += f"""
+    ORDER BY {parse_ordering(ordering)}"""
+    return query
 
 async def get_filtered_data(
     db: Database, params: CLEANSearchQueryParams
@@ -120,7 +152,7 @@ async def get_filtered_data(
     """
 
     # Build the main query
-    query = get_query(columns_to_select, where_clause)
+    query = get_query(columns_to_select, where_clause, ordering=params.ordering)
 
     # Add pagination
     if params.limit is not None:
@@ -142,7 +174,7 @@ async def get_total_count(db: Database, params: CLEANSearchQueryParams) -> int:
     """Get total count of records matching the filters."""
     where_clause, query_params = await build_conditions(params)
 
-    query = get_query("COUNT(*)", where_clause)
+    query = get_query("COUNT(*)", where_clause, include_order_by=False)
 
     # Extract query parameters from the dictionary
     query_args = list(query_params.values())

app/models/query_params.py

@@ -64,6 +64,11 @@ class CLEANSearchQueryParams(BaseModel):
         None, description="Maximum number of records to return"
     )
     offset: Optional[int] = Field(0, description="Number of records to skip")
+    ordering: Optional[str] = Field(
+        None,
+        description="Column to sort by. Prefix with '-' for descending order. "
+        "Allowed values: accession, amino_acids, organism, curation_status, predicted_ec",
+    )
 
 class CLEANTypeaheadQueryParams(BaseModel):
     """Query parameters for CLEAN typeahead suggestions."""

app/routers/search.py

@@ -60,6 +60,11 @@ def parse_query_params(
         None, description="Maximum number of records to return"
     ),
     offset: Optional[int] = Query(0, description="Number of records to skip"),
+    ordering: Optional[str] = Query(
+        None,
+        description="Column to sort by. Prefix with '-' for descending order. "
+        "Allowed values: accession, amino_acids, organism, curation_status, predicted_ec",
+    ),
 ) -> CLEANSearchQueryParams:
     """Parse and validate query parameters."""
     try:
@@ -80,6 +85,7 @@ def parse_query_params(
             format=format,
             limit=limit,
             offset=offset,
+            ordering=ordering,
         )
     except Exception as e:
         logger.error(f"Error parsing query parameters: {e}")
@@ -99,19 +105,14 @@ async def get_data(
     """
 
     try:
-        # # Get total count for the query (without pagination)
-        # total_count = await get_total_count(db, params)
-
-        # # Apply automatic pagination if results exceed threshold and no explicit limit provided
-        # if total_count > settings.AUTO_PAGINATION_THRESHOLD and params.limit is None:
-        #     params.auto_paginated = True
-        #     params.limit = settings.AUTO_PAGINATION_THRESHOLD
-        #     logger.info(
-        #         f"Auto-pagination applied. Results limited to {params.limit} records."
-        #     )
-
-        params.limit = 500
-        # Get data from database (now with potential auto-pagination applied)
+        # Apply default page size if no explicit limit provided
+        if params.limit is None:
+            params.limit = settings.AUTO_PAGINATION_THRESHOLD
+
+        # Get total count for the query (without pagination)
+        total_count = await get_total_count(db, params)
+
+        # Get data from database
         data = await get_filtered_data(db, params)
 
         # Handle response format
@@ -143,12 +144,10 @@ async def get_data(
                 headers={"Content-Disposition": "attachment; filename=CLEAN_data.csv"},
             )
         else:
-            # TODO don't we want total_count to be the value returned by get_total_count?
-            total_count = len(data)
             response = CLEANSearchResponse(
                 total=total_count,
                 offset=params.offset,
-                limit=total_count if total_count < params.limit else params.limit,
+                limit=params.limit,
                 data=[CLEANDataBase(
                     predictions_uniprot_annot_id=record["predictions_uniprot_annot_id"],
                     uniprot=record["uniprot_id"],
@@ -172,54 +171,48 @@ async def get_data(
                 ) for record in data],
             )
 
-            # Add pagination links if automatic pagination was applied
-            if params.auto_paginated:
-                # Add flag indicating automatic pagination was applied
-                response.auto_paginated = True
-
-                if request:
-                    base_url = str(request.url).split("?")[0]
-
-                    # Prepare query parameters for pagination links
-                    # For Pydantic v2 compatibility
-                    query_params = {
-                        k: v
-                        for k, v in params.model_dump().items()
-                        if k not in ["auto_paginated", "offset", "limit"]
-                        and v is not None
+            # Add pagination links
+            if request:
+                base_url = str(request.url).split("?")[0]
+
+                # Prepare query parameters for pagination links
+                query_params = {
+                    k: v
+                    for k, v in params.model_dump().items()
+                    if k not in ["auto_paginated", "offset", "limit"]
+                    and v is not None
+                }
+
+                # Set format explicitly if it was provided
+                if params.format != ResponseFormat.JSON:
+                    query_params["format"] = params.format
+
+                current_offset = params.offset or 0
+                current_limit = params.limit
+
+                # Next page link if there are more records
+                if current_offset + current_limit < total_count:
+                    next_offset = current_offset + current_limit
+                    next_params = {
+                        **query_params,
+                        "offset": next_offset,
+                        "limit": current_limit,
                     }
-
-                    # Set format explicitly if it was provided
-                    if params.format != ResponseFormat.JSON:
-                        query_params["format"] = params.format
-
-                    # Calculate next page link if there are more records
-                    current_offset = params.offset or 0
-                    current_limit = params.limit or total_count
-                    if current_offset + current_limit < total_count:
-                        next_offset = current_offset + current_limit
-                        next_params = {
-                            **query_params,
-                            "offset": next_offset,
-                            "limit": current_limit,
-                        }
-                        response.next = (
-                            f"{base_url}?{urlencode(next_params, doseq=True)}"
-                        )
-
-                    # Calculate previous page link if not on first page
-                    current_offset = params.offset or 0
-                    current_limit = params.limit or total_count
-                    if current_offset > 0:
-                        prev_offset = max(0, current_offset - current_limit)
-                        prev_params = {
-                            **query_params,
-                            "offset": prev_offset,
-                            "limit": current_limit,
-                        }
-                        response.previous = (
-                            f"{base_url}?{urlencode(prev_params, doseq=True)}"
-                        )
+                    response.next = (
+                        f"{base_url}?{urlencode(next_params, doseq=True)}"
+                    )
+
+                # Previous page link if not on first page
+                if current_offset > 0:
+                    prev_offset = max(0, current_offset - current_limit)
+                    prev_params = {
+                        **query_params,
+                        "offset": prev_offset,
+                        "limit": current_limit,
+                    }
+                    response.previous = (
+                        f"{base_url}?{urlencode(prev_params, doseq=True)}"
+                    )
 
             return response