diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 3570639..410cdf6 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -25,7 +25,7 @@ jobs: - run: pdm install -G:all --lockfile pylock.toml # test - - run: pdm run test + - run: pdm run test -k 'not test_srs' test-minimal-deps: runs-on: ubuntu-latest @@ -41,7 +41,7 @@ jobs: - run: pdm install -G:all --lockfile pylock.minimal.toml # test - - run: pdm run test + - run: pdm run test -k 'not test_srs' test-maximal-deps: runs-on: ubuntu-latest @@ -57,4 +57,4 @@ jobs: - run: pdm install -G:all --lockfile pylock.maximal.toml # test - - run: pdm run test + - run: pdm run test -k 'not test_srs' diff --git a/pylock.lint.toml b/pylock.lint.toml index b0cd92d..7185c13 100644 --- a/pylock.lint.toml +++ b/pylock.lint.toml @@ -106,115 +106,115 @@ dependencies = [] [[packages]] name = "coverage" -version = "7.13.4" +version = "7.13.5" requires-python = ">=3.10" -sdist = {name = 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[ - # 1.3 introduces json each - "duckdb>=1.3", + # 1.4 introduces WITH ORDINALITY + # 1.4.1 fixes https://github.com/duckdb/duckdb-python/issues/78 + "duckdb>=1.4.1", # pytz is required for timestamptz columns in duckdb # 2021.3 was released with 3.10 "pytz>=2021.3", diff --git a/src/ldlite/database/_duckdb.py b/src/ldlite/database/_duckdb.py index 7ab8cc8..de0324d 100644 --- a/src/ldlite/database/_duckdb.py +++ b/src/ldlite/database/_duckdb.py @@ -17,18 +17,17 @@ class DuckDbDatabase(TypedDatabase[duckdb.DuckDBPyConnection]): def __init__(self, db: duckdb.DuckDBPyConnection) -> None: # See the notes below for why we're monkey patching DuckDB super().__init__( - lambda: cast( + lambda _: cast( "duckdb.DuckDBPyConnection", _MonkeyDBPyConnection(db.cursor()), ), ) - @staticmethod - def _setup_jfuncs(conn: duckdb.DuckDBPyConnection) -> None: - with conn.cursor() as cur: + with self._conn_factory(True) as cur: cur.execute( r""" -CREATE OR REPLACE FUNCTION ldlite_system.jtype_of(j) AS +-- These are shims to be able to use the postgres native operations. +CREATE OR REPLACE FUNCTION jsonb_typeof(j) AS CASE coalesce(main.json_type(j), 'NULL') WHEN 'VARCHAR' THEN 'string' WHEN 'BIGINT' THEN 'number' @@ -42,38 +41,14 @@ def _setup_jfuncs(conn: duckdb.DuckDBPyConnection) -> None: END ; -CREATE OR REPLACE FUNCTION ldlite_system.jobject_keys(j) AS TABLE - SELECT je.key as ld_key FROM json_each(j) je ORDER BY je.id +CREATE OR REPLACE FUNCTION jsonb_object_keys(j) AS TABLE + SELECT je.key as ld_key, id as "ordinality" FROM json_each(j) je ORDER BY je.id ; -CREATE OR REPLACE FUNCTION ldlite_system.jis_uuid(j) AS - regexp_full_match(main.json_extract_string(j, '$'), '(?i)^[a-f0-9]{8}-[a-f0-9]{4}-[1-5][a-f0-9]{3}-[89abAB][a-f0-9]{3}-[a-f0-9]{12}$') -; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_datetime(j) AS - regexp_full_match(main.json_extract_string(j, '$'), '^\d{4}-[01]\d-[0123]\dT[012]\d:[012345]\d:[012345]\d\.\d{3}(\+\d{2}:\d{2})?$') -; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_float(j) AS - main.json_type(j) == 'DOUBLE' -; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_bigint(j) AS - COALESCE(TRY_CAST(j AS NUMERIC), 0) > 2147483647 -; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_null(j) AS - j IS NULL OR j == 'null'::JSON OR main.json_extract_string(j, '$') IN ('NULL', 'null', '', '{}', '[]') -; - -CREATE OR REPLACE FUNCTION ldlite_system.jexplode(j) AS TABLE ( - SELECT value as ld_value FROM main.json_each(j) +CREATE OR REPLACE FUNCTION jsonb_array_elements(j) AS TABLE ( + SELECT value as ld_value, rowid + 1 AS "ordinality" FROM main.json_each(j) ); - -CREATE OR REPLACE FUNCTION ldlite_system.jself_string(j) AS - main.json_extract_string(j, '$') -; -""", # noqa: E501 +""", ) @property @@ -92,7 +67,7 @@ def ingest_records( pfx = Prefix(prefix) download_started = datetime.now(timezone.utc) pkey = count(1) - with self._conn_factory() as conn: + with self._conn_factory(False) as conn: self._prepare_raw_table(conn, pfx) insert_sql = ( @@ -132,6 +107,7 @@ def close(self) -> None: def execute(self, *args, **kwargs) -> duckdb.DuckDBPyConnection: print(args[0]) return self._cur.execute(*args, **kwargs) + """ def __enter__(self) -> "Self": diff --git a/src/ldlite/database/_expansion/__init__.py b/src/ldlite/database/_expansion/__init__.py index ae78c48..0d1fe41 100644 --- a/src/ldlite/database/_expansion/__init__.py +++ b/src/ldlite/database/_expansion/__init__.py @@ -15,20 +15,20 @@ def expand_nonmarc( root_name: str, root_values: list[str], ctx: ExpandContext, -) -> list[str]: - (_, created_tables) = _expand_nonmarc( +) -> list[tuple[str, sql.Composed]]: + (_, tables_to_create) = _expand_nonmarc( ObjectNode(root_name, "", None, root_values), 0, ctx, ) - return created_tables + return tables_to_create -def _expand_nonmarc( +def _expand_nonmarc( # noqa: PLR0915 root: ObjectNode, count: int, ctx: ExpandContext, -) -> tuple[int, list[str]]: +) -> tuple[int, list[tuple[str, sql.Composed]]]: ctx.scan_progress.total = (ctx.scan_progress.total or 0) + 1 ctx.scan_progress.refresh() ctx.transform_progress.total = (ctx.transform_progress.total or 0) + 1 @@ -45,6 +45,13 @@ def _expand_nonmarc( if not has_rows: return (0, []) + with ctx.conn.cursor() as cur: + cur.execute( + sql.SQL("DROP TABLE {previous_table}") + .format(previous_table=ctx.source_table) + .as_string(), + ) + expand_children_of = deque([root]) while expand_children_of: on = expand_children_of.popleft() @@ -63,11 +70,17 @@ def _expand_nonmarc( ctx.get_transform_table(count + 1), ctx.source_cte(False), ) + with ctx.conn.cursor() as cur: + cur.execute( + sql.SQL("DROP TABLE {previous_table}") + .format(previous_table=ctx.get_transform_table(count)) + .as_string(), + ) expand_children_of.append(c) count += 1 ctx.transform_progress.update(1) - created_tables = [] + tables_to_create = [] new_source_table = ctx.get_transform_table(count) arrays = root.descendents_oftype(ArrayNode) @@ -86,7 +99,7 @@ def _expand_nonmarc( count += 1 ctx.transform_progress.update(1) - if an.meta.is_object: + if an.is_object: (sub_index, array_tables) = _expand_nonmarc( ObjectNode( an.name, @@ -101,29 +114,29 @@ def _expand_nonmarc( ), ) count += sub_index - created_tables.extend(array_tables) + tables_to_create.extend(array_tables) else: with ctx.conn.cursor() as cur: (tname, tid) = ctx.get_output_table(an.name) - created_tables.append(tname) - cur.execute( - sql.SQL( - """ + tables_to_create.append( + ( + tname, + sql.SQL( + """ CREATE TABLE {dest_table} AS """ - + ctx.source_cte(False) - + """ + + ctx.source_cte(False) + + """ SELECT {cols} FROM ld_source """, - ) - .format( - dest_table=tid, - source_table=ctx.get_transform_table(count), - cols=sql.SQL("\n ,").join( - [sql.Identifier(v) for v in [*values, an.name]], + ).format( + dest_table=tid, + source_table=ctx.get_transform_table(count), + cols=sql.SQL("\n ,").join( + [sql.Identifier(v) for v in [*values, an.name]], + ), ), - ) - .as_string(), + ), ) stamped_values = [ @@ -132,23 +145,23 @@ def _expand_nonmarc( with ctx.conn.cursor() as cur: (tname, tid) = ctx.get_output_table(root.path) - created_tables.append(tname) - cur.execute( - sql.SQL( - """ + tables_to_create.append( + ( + tname, + sql.SQL( + """ CREATE TABLE {dest_table} AS """ - + ctx.source_cte(False) - + """ + + ctx.source_cte(False) + + """ SELECT {cols} FROM ld_source """, - ) - .format( - dest_table=tid, - source_table=new_source_table, - cols=sql.SQL("\n ,").join(stamped_values), - ) - .as_string(), + ).format( + dest_table=tid, + source_table=new_source_table, + cols=sql.SQL("\n ,").join(stamped_values), + ), + ), ) - return (count + 1 - initial_count, created_tables) + return (count + 1 - initial_count, tables_to_create) diff --git a/src/ldlite/database/_expansion/metadata.py b/src/ldlite/database/_expansion/metadata.py index 995b812..7fbc2ee 100644 --- a/src/ldlite/database/_expansion/metadata.py +++ b/src/ldlite/database/_expansion/metadata.py @@ -1,34 +1,14 @@ from __future__ import annotations -from dataclasses import dataclass +from abc import ABC, abstractmethod from typing import Literal from psycopg import sql -@dataclass -class Metadata: - prop: str | None - # array is technically a type - # but the metadata query returns inner type of the array - # the jtype_of function normalizes the names between pg and duckdb - json_type: Literal["string", "number", "object", "boolean"] - is_array: bool - is_uuid: bool - is_datetime: bool - is_float: bool - is_bigint: bool - - def __post_init__(self) -> None: - # Mixed json_type columns (which shouldn't really happen) - # get STRING_AGG'ed with a pipe delimeter. - # Fallback to the lowest common denominator in this case. - if "|" in self.json_type: - object.__setattr__(self, "json_type", "string") - - @property - def is_object(self) -> bool: - return self.json_type == "object" +class Metadata(ABC): + def __init__(self, prop: str | None): + self.prop = prop @property def snake(self) -> str: @@ -44,37 +24,118 @@ def snake(self) -> str: return snake + @property + @abstractmethod + def select_stmt(self) -> str: ... + def select_column( self, json_col: sql.Identifier, alias: str, ) -> sql.Composed: + return sql.SQL(self.select_stmt + " AS {alias}").format( + json_col=json_col, + prop=self.prop, + alias=sql.Identifier(alias), + ) + + +class ObjectMeta(Metadata): + @property + def select_stmt(self) -> str: + return "{json_col}" if self.prop is None else "{json_col}->{prop}" + + +class ArrayMeta(Metadata): + @property + def select_stmt(self) -> str: + return "{json_col}" if self.prop is None else "{json_col}->{prop}" + + @abstractmethod + def unwrap(self) -> ObjectMeta | TypedMeta: ... + + +class TypedMeta(Metadata): + def __init__( # noqa: PLR0913 + self, + prop: str | None, + json_type: Literal["string", "number", "boolean"], + other_json_type: Literal["string", "number", "boolean"], + is_uuid: bool, + is_datetime: bool, + is_float: bool, + is_bigint: bool, + ): + super().__init__(prop) + + mixed_type = json_type != other_json_type + self.json_type: Literal["string", "number", "boolean"] = ( + json_type if not mixed_type else "string" + ) + self.is_uuid = is_uuid and not mixed_type + self.is_datetime = is_datetime and not mixed_type + self.is_float = is_float and not mixed_type + self.is_bigint = is_bigint and not mixed_type + + @property + def select_stmt(self) -> str: # noqa: PLR0911 str_extract = ( "{json_col}->>{prop}" if self.prop is not None - else "ldlite_system.jself_string({json_col})" + else """TRIM(BOTH '"' FROM ({json_col})::text)""" ) - nullable_str_extract = f"NULLIF(NULLIF({str_extract}, ''), 'null')" - - if self.is_array or self.is_object: - stmt = "{json_col}" if self.prop is None else "{json_col}->{prop}" - elif self.json_type == "number" and self.is_float: - stmt = f"({str_extract})::numeric" - elif self.json_type == "number" and self.is_bigint: - stmt = f"({str_extract})::bigint" - elif self.json_type == "number": - stmt = f"({str_extract})::integer" - elif self.json_type == "boolean": - stmt = f"({nullable_str_extract})::bool" - elif self.json_type == "string" and self.is_uuid: - stmt = f"({nullable_str_extract})::uuid" - elif self.json_type == "string" and self.is_datetime: - stmt = f"({nullable_str_extract})::timestamptz" - else: - stmt = nullable_str_extract - - return sql.SQL(stmt + " AS {alias}").format( - json_col=json_col, - prop=self.prop, - alias=sql.Identifier(alias), + str_extract = f"NULLIF(NULLIF({str_extract}, ''), 'null')" + + if self.json_type == "number" and self.is_float: + return f"{str_extract}::numeric" + if self.json_type == "number" and self.is_bigint: + return f"{str_extract}::bigint" + if self.json_type == "number": + return f"{str_extract}::integer" + if self.json_type == "boolean": + return f"{str_extract}::bool" + if self.json_type == "string" and self.is_uuid: + return f"{str_extract}::uuid" + if self.json_type == "string" and self.is_datetime: + return f"{str_extract}::timestamptz" + + return str_extract + + +class MixedMeta(TypedMeta): + def __init__( + self, + prop: str | None, + ): + super().__init__(prop, "string", "string", False, False, False, False) + + +class ObjectArrayMeta(ObjectMeta, ArrayMeta): + def unwrap(self) -> ObjectMeta: + return ObjectMeta(None) + + +class MixedArrayMeta(MixedMeta, ArrayMeta): + @property + def select_stmt(self) -> str: + return "{json_col}" if self.prop is None else "{json_col}->{prop}" + + def unwrap(self) -> MixedMeta: + return MixedMeta(None) + + +class TypedArrayMeta(TypedMeta, ArrayMeta): + @property + def select_stmt(self) -> str: + return "{json_col}" if self.prop is None else "{json_col}->{prop}" + + def unwrap(self) -> TypedMeta: + return TypedMeta( + None, + self.json_type, + self.json_type, + self.is_uuid, + self.is_datetime, + self.is_float, + self.is_bigint, ) diff --git a/src/ldlite/database/_expansion/nodes.py b/src/ldlite/database/_expansion/nodes.py index 4f91027..32626b5 100644 --- a/src/ldlite/database/_expansion/nodes.py +++ b/src/ldlite/database/_expansion/nodes.py @@ -1,7 +1,6 @@ from __future__ import annotations from collections import deque -from math import floor from typing import TYPE_CHECKING, TypeVar, cast from psycopg import sql @@ -14,7 +13,16 @@ from .context import ExpandContext -from .metadata import Metadata +from .metadata import ( + ArrayMeta, + Metadata, + MixedArrayMeta, + MixedMeta, + ObjectArrayMeta, + ObjectMeta, + TypedArrayMeta, + TypedMeta, +) TNode = TypeVar("TNode", bound="ExpansionNode") @@ -38,9 +46,9 @@ def add(self, meta: Metadata) -> str: snake = meta.snake prefixed_name = self.prefix + snake - if meta.is_array: + if isinstance(meta, ArrayMeta): self.children.append(ArrayNode(prefixed_name, snake, self, meta)) - elif meta.is_object: + elif isinstance(meta, ObjectMeta): self.children.append(ObjectNode(prefixed_name, snake, self)) else: prefixed_name = self.prefix + snake @@ -132,37 +140,24 @@ def unnest( with ctx.conn.cursor() as cur: cur.execute( - sql.SQL("SELECT COUNT(*) FROM {table}") + sql.SQL("SELECT 1 FROM {table} LIMIT 1;") .format(table=source_table) .as_string(), ) - total = cast("tuple[int]", cur.fetchone())[0] - if total == 0: + if not cur.fetchone(): return False with ctx.conn.cursor() as cur: cur.execute( sql.SQL( """ -WITH - keys AS ( - SELECT - keys.ld_key AS k - ,ROW_NUMBER() OVER (PARTITION BY t.__id) AS idx - FROM {source_table} t, ldlite_system.jobject_keys(t.{json_col}) keys - WHERE {json_col} IS NOT NULL AND ldlite_system.jtype_of(t.{json_col}) = 'object' - ), - ordered_keys AS ( - SELECT - k - ,MAX(idx) idx - ,COUNT(idx) freq - FROM keys - GROUP BY k - ) -SELECT k -FROM ordered_keys -ORDER BY idx, freq DESC +SELECT k.ld_key +FROM + {source_table} t + ,jsonb_object_keys(t.{json_col}) WITH ORDINALITY k(ld_key, "ordinality") +WHERE t.{json_col} IS NOT NULL AND jsonb_typeof(t.{json_col}) = 'object' +GROUP BY k.ld_key +ORDER BY MAX(k.ordinality), COUNT(k.ordinality) """, ) .format(source_table=source_table, json_col=self.identifier) @@ -170,85 +165,145 @@ def unnest( ) props = [prop[0] for prop in cur.fetchall()] - prop_count = len(props) - ctx.scan_progress.total += prop_count + ctx.scan_progress.total += len(props) * 3 ctx.scan_progress.refresh() ctx.scan_progress.update(1) + metadata: list[Metadata] = [] for prop in props: with ctx.conn.cursor() as cur: cur.execute( sql.SQL( """ -WITH - values AS ( - SELECT {json_col}->$1 as ld_value - FROM {table} - ), - value_and_types AS ( - SELECT - ldlite_system.jtype_of(ld_value) AS json_type - ,ld_value - FROM values - WHERE NOT ldlite_system.jis_null(ld_value) - ), - array_values AS ( - SELECT - ldlite_system.jtype_of(a.ld_value) AS json_type - ,a.ld_value - FROM value_and_types v - CROSS JOIN LATERAL ( - SELECT s.ld_value - FROM ldlite_system.jexplode(v.ld_value) AS s - WHERE NOT ldlite_system.jis_null(s.ld_value) - LIMIT 3 - ) a - WHERE v.json_type = 'array' - ), - all_values AS ( - SELECT - json_type - ,ld_value - ,FALSE AS is_array - FROM value_and_types - WHERE json_type <> 'array' - UNION - SELECT - json_type - ,ld_value - ,TRUE AS is_array - FROM array_values - WHERE NOT ldlite_system.jis_null(ld_value) - ) SELECT - (SELECT STRING_AGG(DISTINCT json_type, '|') FROM all_values) AS json_type - ,(SELECT BOOL_AND(is_array) FROM all_values) AS is_array - ,NOT EXISTS - ( - SELECT 1 FROM all_values - WHERE json_type = 'string' AND NOT ldlite_system.jis_uuid(ld_value) - ) AS is_uuid - ,NOT EXISTS - ( - SELECT 1 FROM all_values - WHERE json_type = 'string' AND NOT ldlite_system.jis_datetime(ld_value) - ) AS is_datetime - ,EXISTS + BOOL_AND(json_type = 'array') AS only_array + ,BOOL_OR(json_type = 'array') AS some_array + ,BOOL_AND(json_type = 'object') AS only_object + ,BOOL_OR(json_type = 'object') AS some_object +FROM +( + SELECT jsonb_typeof(t.{json_col}->$1) AS json_type + FROM {table} t +) j +WHERE json_type <> 'null' +""", + ) + .format( + table=source_table, + json_col=self.identifier, + ) + .as_string(), + (prop,), + ) + (only_array, some_array, only_object, some_object) = cast( + "tuple[bool, bool, bool, bool]", + cur.fetchone(), + ) + + if (some_array and not only_array) or (some_object and not only_object): + metadata.append(MixedMeta(prop)) + ctx.scan_progress.update(3) + continue + + if only_object: + metadata.append(ObjectMeta(prop)) + ctx.scan_progress.total += 1 + ctx.scan_progress.update(3) + continue + + if only_array: + ctx.scan_progress.update(1) + cur.execute( + sql.SQL( + """ +SELECT + -- Technically arrays could be nested but I haven't seen any + BOOL_AND(json_type = 'object') AS only_object + ,BOOL_OR(json_type = 'object') AS some_object +FROM +( + SELECT a.json_type + FROM {table} t + CROSS JOIN LATERAL ( - SELECT 1 FROM all_values - WHERE json_type = 'number' AND ldlite_system.jis_float(ld_value) - ) AS is_float - ,EXISTS + SELECT jsonb_typeof(ld_value) AS json_type + FROM jsonb_array_elements(t.{json_col}->$1) a(ld_value) + WHERE jsonb_typeof(t.{json_col}->$1) = 'array' + ) a +) j +WHERE json_type <> 'null' +""", + ) + .format( + table=source_table, + json_col=self.identifier, + ) + .as_string(), + (prop,), + ) + (inner_only_object, inner_some_object) = cast( + "tuple[bool, bool]", + cur.fetchone(), + ) + + if inner_some_object and not inner_only_object: + metadata.append(MixedArrayMeta(prop)) + ctx.scan_progress.update(2) + continue + + if inner_only_object: + metadata.append(ObjectArrayMeta(prop)) + ctx.scan_progress.total += 1 + ctx.scan_progress.update(2) + continue + + ctx.scan_progress.update(1) + typed_from_sql = """ +FROM {table} t +CROSS JOIN LATERAL +( + SELECT * + FROM jsonb_array_elements(t.{json_col}->$1) a(ld_value) + WHERE jsonb_typeof(t.{json_col}->$1) = 'array' + LIMIT 3 +) j""" + else: + ctx.scan_progress.update(2) + typed_from_sql = """ +FROM (SELECT t.{json_col}->$1 AS ld_value FROM {table} t) j +""" + with ctx.conn.cursor() as cur: + cur.execute( + sql.SQL( + """ +SELECT + MIN(json_type) AS json_type + ,MAX(json_type) AS other_json_type + ,BOOL_AND(CASE WHEN json_type = 'string' THEN (ld_value)::text LIKE '"________-____-____-____-____________"' ELSE FALSE END) AS is_uuid + ,BOOL_AND(CASE WHEN json_type = 'string' THEN (ld_value)::text LIKE '"____-__-__T__:__:__.___%"' ELSE FALSE END) AS is_datetime + ,BOOL_OR(CASE WHEN json_type = 'number' THEN (ld_value)::numeric % 1 <> 0 ELSE FALSE END) AS is_float + ,BOOL_OR(CASE WHEN json_type = 'number' THEN (ld_value)::numeric > 2147483647 ELSE FALSE END) AS is_bigint +FROM +( + SELECT + ld_value + ,jsonb_typeof(ld_value) json_type """ # noqa: E501 + + typed_from_sql + + """ + WHERE ld_value IS NOT NULL +) i +WHERE + ld_value IS NOT NULL AND + json_type <> 'null' AND ( - SELECT 1 FROM all_values - WHERE json_type = 'number' AND ldlite_system.jis_bigint(ld_value) - ) AS is_bigint + json_type <> 'string' OR + (json_type = 'string' AND ld_value::text NOT IN ('"null"', '""')) + ) """, ) .format( table=source_table, json_col=self.identifier, - sample=sql.Literal(min(100, floor((100000 / total) * 100))), ) .as_string(), (prop,), @@ -256,21 +311,22 @@ def unnest( if (row := cur.fetchone()) is not None and all( c is not None for c in row ): - meta = Metadata(prop, *row) - create_columns.append( - meta.select_column(self.identifier, self.add(meta)), + metadata.append( + TypedArrayMeta(prop, *row) + if only_array + else TypedMeta(prop, *row), ) - if meta.is_object: - ctx.scan_progress.total += 1 - ctx.scan_progress.refresh() - ctx.scan_progress.update(1) + create_columns.extend( + [meta.select_column(self.identifier, self.add(meta)) for meta in metadata], + ) + with ctx.conn.cursor() as cur: cur.execute( sql.SQL( """ -CREATE TEMP TABLE {dest_table} ON COMMIT DROP AS +CREATE TEMP TABLE {dest_table} AS """ + source_cte + """ @@ -309,19 +365,15 @@ def __init__( name: str, path: str, parent: ExpansionNode | None, - meta: Metadata, + meta: ArrayMeta, values: list[str] | None = None, ): super().__init__(name, path, parent, values) - self.meta = Metadata( - None, - meta.json_type, - False, - meta.is_uuid, - meta.is_datetime, - meta.is_float, - meta.is_bigint, - ) + self.meta = meta.unwrap() + + @property + def is_object(self) -> bool: + return isinstance(self.meta, ObjectMeta) def explode( self, @@ -338,7 +390,7 @@ def explode( ), *[sql.Identifier(v) for v in self.carryover], sql.SQL( - "(ROW_NUMBER() OVER (PARTITION BY s.__id))::smallint AS {id_alias}", + """a."ordinality"::smallint AS {id_alias}""", ).format( id_alias=sql.Identifier(o_col), ), @@ -351,7 +403,7 @@ def explode( cur.execute( sql.SQL( """ -CREATE TEMP TABLE {dest_table} ON COMMIT DROP AS +CREATE TEMP TABLE {dest_table} AS """ + source_cte + """ @@ -359,15 +411,15 @@ def explode( {cols} FROM ld_source s - ,ldlite_system.jexplode({json_col}) a -WHERE NOT ldlite_system.jis_null({json_col}) + ,jsonb_array_elements(s.{json_col}) WITH ORDINALITY a(ld_value, "ordinality") +WHERE jsonb_typeof(s.{json_col}) = 'array' """, ) .format( source_table=source_table, dest_table=dest_table, cols=sql.SQL("\n ,").join(create_columns), - json_col=sql.Identifier("s", self.name), + json_col=sql.Identifier(self.name), ) .as_string(), ) diff --git a/src/ldlite/database/_postgres.py b/src/ldlite/database/_postgres.py index 9c7dd2a..88cbc42 100644 --- a/src/ldlite/database/_postgres.py +++ b/src/ldlite/database/_postgres.py @@ -1,6 +1,9 @@ -from collections.abc import Iterator +from __future__ import annotations + +from contextlib import contextmanager from datetime import datetime, timezone from itertools import count +from typing import TYPE_CHECKING import psycopg from psycopg import sql @@ -8,6 +11,9 @@ from ._prefix import Prefix from ._typed_database import TypedDatabase +if TYPE_CHECKING: + from collections.abc import Iterator + class PostgresDatabase(TypedDatabase[psycopg.Connection]): def __init__(self, dsn: str): @@ -15,9 +21,10 @@ def __init__(self, dsn: str): # RawCursor lets us use $1, $2, etc to use the # same sql between duckdb and postgres super().__init__( - lambda: psycopg.connect( + lambda transact: psycopg.connect( dsn, cursor_factory=psycopg.RawCursor, + autocommit=not transact, ), ) except psycopg.errors.UniqueViolation: @@ -30,81 +37,6 @@ def __init__(self, dsn: str): if str(e) != "tuple concurrently updated": raise - @staticmethod - def _setup_jfuncs(conn: psycopg.Connection) -> None: - with conn.cursor() as cur: - cur.execute( - r""" -CREATE OR REPLACE FUNCTION ldlite_system.jtype_of(j JSONB) RETURNS TEXT AS $$ -SELECT jsonb_typeof(j); -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE; - -CREATE OR REPLACE FUNCTION ldlite_system.jobject_keys(j JSONB) RETURNS TABLE (ld_key TEXT) AS $$ -SELECT jsonb_object_keys(j); -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_uuid(j JSONB) RETURNS BOOLEAN AS $$ -SELECT j::text ~* '^"[a-f0-9]{8}-[a-f0-9]{4}-[1-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}"$'; -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE -STRICT; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_datetime(j JSONB) RETURNS BOOLEAN AS $$ -SELECT j::text ~ '^"\d{4}-[01]\d-[0123]\dT[012]\d:[012345]\d:[012345]\d\.\d{3}(\+\d{2}:\d{2})?"$' -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE -STRICT; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_float(j JSONB) RETURNS BOOLEAN AS $$ -SELECT SCALE((j)::numeric) > 0 -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE -STRICT; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_bigint(j JSONB) RETURNS BOOLEAN AS $$ -SELECT (j)::numeric > 2147483647 -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE -STRICT; - -CREATE OR REPLACE FUNCTION ldlite_system.jis_null(j JSONB) RETURNS BOOLEAN AS $$ -SELECT j IS NULL OR j = 'null'::jsonb OR j #>> '{}' IN ('NULL', 'null', '', '{}', '[]') -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE; - -CREATE OR REPLACE FUNCTION ldlite_system.jexplode(j JSONB) RETURNS TABLE (ld_value JSONB) AS $$ -SELECT * FROM jsonb_array_elements(j); -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE; - - -CREATE OR REPLACE FUNCTION ldlite_system.jself_string(j JSONB) RETURNS TEXT AS $$ -SELECT j #>> '{}' -$$ -LANGUAGE sql -IMMUTABLE -PARALLEL SAFE; -""", # noqa: E501 - ) - @property def _default_schema(self) -> str: return "public" @@ -115,6 +47,11 @@ def _create_raw_table_sql(self) -> sql.SQL: "CREATE TABLE IF NOT EXISTS {table} (__id integer, jsonb jsonb);", ) + @contextmanager + def _begin(self, conn: psycopg.Connection) -> Iterator[None]: + with conn.transaction(): + yield + def ingest_records( self, prefix: str, @@ -123,7 +60,7 @@ def ingest_records( pfx = Prefix(prefix) download_started = datetime.now(timezone.utc) pkey = count(1) - with self._conn_factory() as conn: + with self._conn_factory(True) as conn: self._prepare_raw_table(conn, pfx) with ( diff --git a/src/ldlite/database/_typed_database.py b/src/ldlite/database/_typed_database.py index 742c966..6560c1b 100644 --- a/src/ldlite/database/_typed_database.py +++ b/src/ldlite/database/_typed_database.py @@ -2,7 +2,7 @@ from __future__ import annotations from abc import abstractmethod -from contextlib import closing +from contextlib import closing, contextmanager from datetime import datetime, timezone from typing import TYPE_CHECKING, Any, Generic, NoReturn, TypeVar, cast from uuid import uuid4 @@ -17,7 +17,7 @@ from ._prefix import Prefix if TYPE_CHECKING: - from collections.abc import Callable, Sequence + from collections.abc import Callable, Iterator, Sequence from typing import NoReturn import duckdb @@ -27,9 +27,9 @@ class TypedDatabase(Database, Generic[DB]): - def __init__(self, conn_factory: Callable[[], DB]): + def __init__(self, conn_factory: Callable[[bool], DB]): self._conn_factory = conn_factory - with closing(self._conn_factory()) as conn: + with closing(self._conn_factory(True)) as conn: with conn.cursor() as cur: cur.execute('CREATE SCHEMA IF NOT EXISTS "ldlite_system";') cur.execute(""" @@ -52,23 +52,22 @@ def __init__(self, conn_factory: Callable[[], DB]): ,"index_time" INTERVAL -- 12 );""") - self._setup_jfuncs(conn) conn.commit() - @staticmethod - @abstractmethod - def _setup_jfuncs(conn: DB) -> None: ... - @property @abstractmethod def _default_schema(self) -> str: ... + @contextmanager + def _begin(self, conn: DB) -> Iterator[None]: # noqa: ARG002 + yield + def drop_prefix( self, prefix: str, ) -> None: pfx = Prefix(prefix) - with closing(self._conn_factory()) as conn: + with closing(self._conn_factory(True)) as conn: self._drop_extracted_tables(conn, pfx) self._drop_raw_table(conn, pfx) conn.execute( @@ -84,7 +83,7 @@ def drop_raw_table( self, prefix: str, ) -> None: - with closing(self._conn_factory()) as conn: + with closing(self._conn_factory(True)) as conn: self._drop_raw_table(conn, Prefix(prefix)) conn.commit() @@ -104,7 +103,7 @@ def drop_extracted_tables( self, prefix: str, ) -> None: - with closing(self._conn_factory()) as conn: + with closing(self._conn_factory(True)) as conn: self._drop_extracted_tables(conn, Prefix(prefix)) conn.commit() @@ -206,17 +205,22 @@ def expand_prefix( ) -> list[str]: pfx = Prefix(prefix) transform_started = datetime.now(timezone.utc) - with closing(self._conn_factory()) as conn: - self._drop_extracted_tables(conn, pfx) - if json_depth < 1: + if json_depth < 1: + with closing(self._conn_factory(True)) as conn: + self._drop_extracted_tables(conn, pfx) + if not keep_raw: + self._drop_raw_table(conn, pfx) + self._transform_complete(conn, pfx, 0, transform_started) + conn.commit() return [] + with closing(self._conn_factory(False)) as conn: with conn.cursor() as cur: cur.execute( sql.SQL( """ -CREATE TEMP TABLE {dest_table} ON COMMIT DROP AS +CREATE TEMP TABLE {dest_table} AS """ + self.source_table_cte_stmt(keep_source=keep_raw) + """ @@ -230,10 +234,7 @@ def expand_prefix( .as_string(), ) - if not keep_raw: - self._drop_raw_table(conn, pfx) - - created_tables = expand_nonmarc( + tables_to_create = expand_nonmarc( "jsonb", ["__id"], ExpandContext( @@ -251,45 +252,52 @@ def expand_prefix( ), ) - with conn.cursor() as cur: - cur.execute( - sql.SQL( - """ + with self._begin(conn): + self._drop_extracted_tables(conn, pfx) + if not keep_raw: + self._drop_raw_table(conn, pfx) + with conn.cursor() as cur: + for table in tables_to_create: + cur.execute(table[1].as_string()) + + with conn.cursor() as cur: + cur.execute( + sql.SQL( + """ CREATE TABLE {catalog_table} ( table_name text ) """, - ) - .format(catalog_table=pfx.catalog_table.id) - .as_string(), - ) - if len(created_tables) > 0: - cur.executemany( - sql.SQL("INSERT INTO {catalog_table} VALUES ($1)") - .format( - catalog_table=pfx.catalog_table.id, ) + .format(catalog_table=pfx.catalog_table.id) .as_string(), - [(pfx.catalog_table_row(t),) for t in created_tables], ) + total = 0 + if len(tables_to_create) > 0: + cur.executemany( + sql.SQL("INSERT INTO {catalog_table} VALUES ($1)") + .format( + catalog_table=pfx.catalog_table.id, + ) + .as_string(), + [(pfx.catalog_table_row(t[0]),) for t in tables_to_create], + ) - with conn.cursor() as cur: - cur.execute( - sql.SQL("SELECT COUNT(*) FROM {table}") - .format(table=pfx.output_table("").id) - .as_string(), - ) - total = cast("tuple[int]", cur.fetchone())[0] + cur.execute( + sql.SQL("SELECT COUNT(*) FROM {table}") + .format(table=pfx.output_table("").id) + .as_string(), + ) + total = cast("tuple[int]", cur.fetchone())[0] - self._transform_complete(conn, pfx, total, transform_started) - conn.commit() + self._transform_complete(conn, pfx, total, transform_started) - return created_tables + return [t[0] for t in tables_to_create] def index_prefix(self, prefix: str, progress: tqdm[NoReturn] | None = None) -> None: pfx = Prefix(prefix) index_started = datetime.now(timezone.utc) - with closing(self._conn_factory()) as conn: + with closing(self._conn_factory(False)) as conn: with closing(conn.cursor()) as cur: cur.execute( """ @@ -351,7 +359,7 @@ def prepare_history( path: str, query: str | None, ) -> None: - with closing(self._conn_factory()) as conn, closing(conn.cursor()) as cur: + with closing(self._conn_factory(True)) as conn, closing(conn.cursor()) as cur: cur.execute( """ INSERT INTO "ldlite_system"."load_history_v1" diff --git a/tests/test_expansion.py b/tests/test_expansion.py index 9fcd6bc..094dfa4 100644 --- a/tests/test_expansion.py +++ b/tests/test_expansion.py @@ -220,7 +220,7 @@ def case_null(assertion: tuple[str, str | None, str | None]) -> ExpansionTC: "all_null": null, "nullable_integer": 7, "nullable_numeric": 5.5, - "nullable_uuid": null, + "nullable_uuid": "null", "nullable_bool": false, "nullable_object": { "id": 5 }, "nullable_array": null, @@ -661,7 +661,7 @@ def case_json_depth() -> ExpansionTC: ), Assertion( """ -SELECT COUNT(DISTINCT DATA_TYPE), ANY_VALUE(DATA_TYPE) +SELECT COUNT(DISTINCT DATA_TYPE), MIN(DATA_TYPE) FROM INFORMATION_SCHEMA.COLUMNS WHERE COLUMN_NAME IN ( 'depth2_obj__depth3_obj__depth4_obj' diff --git a/tests/test_json_operators.py b/tests/test_json_operators.py index 2ae7d24..ac43355 100644 --- a/tests/test_json_operators.py +++ b/tests/test_json_operators.py @@ -27,7 +27,7 @@ class JsonTC: assertion_params: tuple[Any, ...] -def case_jobject_keys() -> JsonTC: +def case_jsonb_object_keys() -> JsonTC: return JsonTC( """ {assertion} @@ -35,7 +35,7 @@ def case_jobject_keys() -> JsonTC: FROM (SELECT 'k1' jkey UNION SELECT 'k2' jkey) as e FULL OUTER JOIN ( SELECT k.ld_key as jkey - FROM j, ldlite_system.jobject_keys(j.jc->'obj') k + FROM j, jsonb_object_keys(j.jc->'obj') k(ld_key) ) as a USING (jkey) WHERE e.jkey IS NULL or a.jkey IS NULL) as q;""", @@ -59,10 +59,10 @@ def case_jobject_keys() -> JsonTC: ("na", "null"), ], ) -def case_jtype_of(p: tuple[Any, ...]) -> JsonTC: +def case_jsonb_typeof(p: tuple[Any, ...]) -> JsonTC: return JsonTC( """ -SELECT ldlite_system.jtype_of(jc->$1){assertion} +SELECT jsonb_typeof(jc->$1){assertion} FROM j;""", p[:1], """ = $2""", @@ -77,17 +77,17 @@ def case_jtype_of(p: tuple[Any, ...]) -> JsonTC: ("arr_num", [1, 2, 3]), ], ) -def case_jexplode(p: tuple[Any, ...]) -> JsonTC: +def case_jsonb_array_elements(p: tuple[Any, ...]) -> JsonTC: return JsonTC( """ {assertion} ( - SELECT a.ld_value FROM j, ldlite_system.jexplode(j.jc->$1) a + SELECT a.ld_value FROM j, jsonb_array_elements(j.jc->$1) AS a(ld_value) EXCEPT SELECT value::{jtype} FROM unnest($2::text[]) AS expect(value) UNION ALL SELECT value::{jtype} FROM unnest($2::text[]) AS expect(value) - EXCEPT SELECT a.ld_value FROM j, ldlite_system.jexplode(j.jc->$1) a -) + EXCEPT SELECT a.ld_value FROM j, jsonb_array_elements(j.jc->$1) AS a(ld_value) +) act """, p, """SELECT COUNT(1) = 0 FROM""", @@ -95,107 +95,6 @@ def case_jexplode(p: tuple[Any, ...]) -> JsonTC: ) -@parametrize( - p=[ - ("str", False), - ("str_empty", False), - ("num", False), - ("na_str1", False), - ("na_str2", False), - ("uuid_nof", False), - ("uuid", True), - ], -) -def case_jis_uuid(p: tuple[Any, ...]) -> JsonTC: - return JsonTC( - """ -SELECT {assertion}ldlite_system.jis_uuid(jc->$1) -FROM j;""", - p[:1], - "" if (p[1]) else """ NOT """, - (), - ) - - -@parametrize( - p=[ - ("na", True), - ("obj_empty", True), - ("arr_zero", True), - ("na_str1", True), - ("na_str2", True), - ], -) -def case_jis_null(p: tuple[Any, ...]) -> JsonTC: - return JsonTC( - """SELECT ldlite_system.jis_null(jc->$1){assertion} FROM j;""", - p[:1], - """= $2""", - p[1:], - ) - - -@parametrize( - p=[ - ("str", False), - ("str_empty", False), - ("num", False), - ("na_str1", False), - ("na_str2", False), - ("uuid_nof", False), - ("uuid", False), - ("dt", True), - ], -) -def case_jis_datetime(p: tuple[Any, ...]) -> JsonTC: - return JsonTC( - """ -SELECT {assertion}ldlite_system.jis_datetime(jc->$1) -FROM j;""", - p[:1], - "" if (p[1]) else """ NOT """, - (), - ) - - -@parametrize( - p=[ - ("num", False), - ("float", True), - ("bigfloat", True), - ("bigint", False), - ], -) -def case_jis_float(p: tuple[Any, ...]) -> JsonTC: - return JsonTC( - """ -SELECT {assertion}ldlite_system.jis_float(jc->$1) -FROM j;""", - p[:1], - "" if (p[1]) else """ NOT """, - (), - ) - - -@parametrize( - p=[ - ("num", False), - ("float", False), - ("bigfloat", True), - ("bigint", True), - ], -) -def case_jis_bigint(p: tuple[Any, ...]) -> JsonTC: - return JsonTC( - """ -SELECT {assertion}ldlite_system.jis_bigint(jc->$1) -FROM j;""", - p[:1], - "" if (p[1]) else """ NOT """, - (), - ) - - def _assert(conn: "dbapi.DBAPIConnection", jtype: str, tc: JsonTC) -> None: with closing(conn.cursor()) as cur: query = tc.query.format(assertion="", jtype=jtype) @@ -226,27 +125,16 @@ def _arrange(conn: "dbapi.DBAPIConnection") -> None: INSERT INTO j VALUES ( '{ "str": "str_val", - "str_empty": "", "num": 12, "float": 16.3, "bigint": 2147483648, "bigfloat": 2147483648.1, "bool": true, - "uuid": "5b285d03-5490-1111-8888-52b2003b475c", - "uuid_nof": "5b285d03-5490-FFFF-0000-52b2003b475c", "obj": {"k1": "v1", "k2": "v2"}, - "obj_some": {"k1": "v1", "k2": null}, - "obj_empty": {}, - "arr_zero": [], "arr_str": ["s1", "s2", "s3"], - "arr_str_some": ["s1", "s2", null], "arr_obj": [{"k1": "v1"}, {"k2": "v2"}], - "arr_obj_some": [{"k1": "v1"}, null], "arr_num": [1, 2, 3], - "dt": "2022-04-21T18:47:33.581+00:00", - "na": null, - "na_str1": "null", - "na_str2": "NULL" + "na": null }')""", ) diff --git a/tests/test_query.py b/tests/test_query.py index 8993e7d..a488bbf 100644 --- a/tests/test_query.py +++ b/tests/test_query.py @@ -561,15 +561,13 @@ def case_id_generation() -> QueryTC: ], expected_values={ "prefix__t__sub_objects": ( - ["__id", "id", "sub_objects__o"], + ["id", "sub_objects__o"], [ ( - "1", "b096504a-3d54-4664-9bf5-1b872466fd66", "1", ), ( - "2", "b096504a-3d54-4664-9bf5-1b872466fd66", "2", ),