Try to speed up CSV writing

nomenklatura/statement/serialize.py

@@ -2,7 +2,7 @@
 from io import TextIOWrapper
 from pathlib import Path
 from types import TracebackType
-from typing import BinaryIO, Generator, Iterable, List, Optional, Type
+from typing import BinaryIO, Generator, Iterable, List, Optional, TextIO, Type
 
 import click
 import orjson
@@ -16,6 +16,7 @@
 PACK = "pack"
 FORMATS = [JSON, CSV, PACK]
 
+CSV_BATCH = 5000
 CSV_COLUMNS = [
     "canonical_id",
     "entity_id",
@@ -108,9 +109,11 @@ def read_path_statements(
 
 def get_statement_writer(fh: BinaryIO, format: str) -> "StatementWriter":
     if format == CSV:
-        return CSVStatementWriter(fh)
+        wrapped = TextIOWrapper(fh, encoding="utf-8")
+        return CSVStatementWriter(wrapped)
     elif format == PACK:
-        return PackStatementWriter(fh)
+        wrapped = TextIOWrapper(fh, encoding="utf-8")
+        return PackStatementWriter(wrapped)
     elif format == JSON:
         return JSONStatementWriter(fh)
     raise RuntimeError("Unknown statement format: %s" % format)
@@ -124,14 +127,11 @@ def write_statements(fh: BinaryIO, format: str, statements: Iterable[S]) -> None
 
 
 class StatementWriter(object):
-    def __init__(self, fh: BinaryIO) -> None:
-        self.fh = fh
-
     def write(self, stmt: S) -> None:
         raise NotImplementedError()
 
     def close(self) -> None:
-        self.fh.close()
+        raise NotImplementedError()
 
     def __enter__(self) -> "StatementWriter":
         return self
@@ -146,37 +146,47 @@ def __exit__(
 
 
 class JSONStatementWriter(StatementWriter):
+    def __init__(self, fh: BinaryIO) -> None:
+        self.fh = fh
+
     def write(self, stmt: S) -> None:
         data = stmt.to_dict()
         out = orjson.dumps(data, option=orjson.OPT_APPEND_NEWLINE)
         self.fh.write(out)
 
+    def close(self) -> None:
+        self.fh.close()
+
 
 class CSVStatementWriter(StatementWriter):
-    def __init__(self, fh: BinaryIO) -> None:
-        super().__init__(fh)
-        self.wrapper = TextIOWrapper(fh, encoding="utf-8")
-        self.writer = csv.writer(self.wrapper, dialect=csv.unix_dialect)
+    def __init__(self, fh: TextIO) -> None:
+        self.fh = fh
+        self.writer = csv.writer(self.fh, dialect=csv.unix_dialect)
         self.writer.writerow(CSV_COLUMNS)
+        self._batch: List[List[Optional[str]]] = []
 
     def write(self, stmt: S) -> None:
         row = stmt.to_csv_row()
-        self.writer.writerow([row.get(c) for c in CSV_COLUMNS])
+        self._batch.append([row.get(c) for c in CSV_COLUMNS])
+        if len(self._batch) >= CSV_BATCH:
+            self.writer.writerows(self._batch)
+            self._batch.clear()
 
     def close(self) -> None:
-        self.wrapper.close()
-        super().close()
+        if len(self._batch) > 0:
+            self.writer.writerows(self._batch)
+        self.fh.close()
 
 
 class PackStatementWriter(StatementWriter):
-    def __init__(self, fh: BinaryIO) -> None:
-        super().__init__(fh)
-        self.wrapper = TextIOWrapper(fh, encoding="utf-8")
+    def __init__(self, fh: TextIO) -> None:
+        self.fh = fh
         self.writer = csv.writer(
-            self.wrapper,
+            self.fh,
             dialect=csv.unix_dialect,
             quoting=csv.QUOTE_MINIMAL,
         )
+        self._batch: List[List[Optional[str]]] = []
 
     def write(self, stmt: S) -> None:
         row = stmt.to_csv_row()
@@ -185,8 +195,12 @@ def write(self, stmt: S) -> None:
         if prop is None or schema is None:
             raise ValueError("Cannot pack statement without prop and schema")
         row["prop"] = pack_prop(schema, prop)
-        self.writer.writerow([row.get(c) for c in PACK_COLUMNS])
+        self._batch.append([row.get(c) for c in PACK_COLUMNS])
+        if len(self._batch) >= CSV_BATCH:
+            self.writer.writerows(self._batch)
+            self._batch.clear()
 
     def close(self) -> None:
-        self.wrapper.close()
-        super().close()
+        if len(self._batch) > 0:
+            self.writer.writerows(self._batch)
+        self.fh.close()

nomenklatura/store/level.py

@@ -158,7 +158,7 @@ def __init__(
     ) -> None:
         super().__init__(store, scope, external=external)
         self.store: LevelDBStore[DS, CE] = store
-        self.last_seens: Dict[str, str] = {}
+        self.last_seens: Dict[str, Optional[str]] = {}
 
     def has_entity(self, id: str) -> bool:
         prefix = b(f"s:{id}:")
@@ -188,7 +188,10 @@ def get_entity(self, id: str) -> Optional[CE]:
                 for v in it:
                     statements.append(unpack_statement(v, id, True))
         for stmt in statements:
-            if stmt.dataset not in self.last_seens:
+            if (
+                stmt.dataset not in self.last_seens
+                or self.last_seens[stmt.dataset] is None
+            ):
                 ls_val = self.store.db.get(b(f"ls:{stmt.dataset}"))
                 ls = ls_val.decode("utf-8") if ls_val is not None else None
                 self.last_seens[stmt.dataset] = ls