From 1125774293038664224dcca1f2dc9ed4974118fc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 5 Aug 2024 16:46:13 +0000 Subject: [PATCH 01/51] build(deps): Bump singer-sdk from 0.38.0 to 0.39.0 (#475) --- poetry.lock | 36 +++++++++--------------------------- pyproject.toml | 2 +- tap_postgres/client.py | 7 ++++--- 3 files changed, 14 insertions(+), 31 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1af8478d..1c27928c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1111,23 +1111,6 @@ snowballstemmer = ">=2.2.0" [package.extras] toml = ["tomli (>=1.2.3)"] -[[package]] -name = "pyjwt" -version = "2.8.0" -description = "JSON Web Token implementation in Python" -optional = false -python-versions = ">=3.7" -files = [ - {file = "PyJWT-2.8.0-py3-none-any.whl", hash = "sha256:59127c392cc44c2da5bb3192169a91f429924e17aff6534d70fdc02ab3e04320"}, - {file = "PyJWT-2.8.0.tar.gz", hash = "sha256:57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de"}, -] - -[package.extras] -crypto = ["cryptography (>=3.4.0)"] -dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"] -docs = ["sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"] -tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] - [[package]] name = "pynacl" version = "1.5.0" @@ -1603,30 +1586,28 @@ files = [ [[package]] name = "singer-sdk" -version = "0.38.0" +version = "0.39.0" description = "A framework for building Singer taps" optional = false python-versions = ">=3.8" files = [ - {file = "singer_sdk-0.38.0-py3-none-any.whl", hash = "sha256:c8be06edae149571df907262ce870dca990dc86a588609dec4ee8404aed3dc01"}, - {file = "singer_sdk-0.38.0.tar.gz", hash = "sha256:22f13980f9d5d26b98c2654a28e30ddda92d334eade6c50b6a0668be5a8aa55b"}, + {file = "singer_sdk-0.39.0-py3-none-any.whl", hash = "sha256:5b5aa4b485c360fb70af88c5d003b37b74c21c102adac21ea49fa023de860a23"}, + {file = "singer_sdk-0.39.0.tar.gz", hash = "sha256:e5ab6975e44324be32d15e75e86cb2d6719fc6f6d4b95ee0670a8a70c70d73bc"}, ] [package.dependencies] backoff = {version = ">=2.0.0", markers = "python_version < \"4\""} backports-datetime-fromisoformat = {version = ">=2.0.1", markers = "python_version < \"3.11\""} click = ">=8.0,<9.0" -cryptography = ">=3.4.6" fs = ">=2.4.16" -importlib-metadata = {version = "<8.0.0", markers = "python_version < \"3.12\""} -importlib-resources = {version = ">=5.12.0,<6.2.0 || >6.2.0,<6.3.0 || >6.3.0,<6.3.1 || >6.3.1", markers = "python_version < \"3.9\""} +importlib-metadata = {version = "<9.0.0", markers = "python_version < \"3.12\""} +importlib-resources = {version = ">=5.12.0,<6.2.0 || >6.2.0,<6.3.0 || >6.3.0,<6.3.1 || >6.3.1", markers = "python_version < \"3.10\""} inflection = ">=0.5.1" joblib = ">=1.3.0" jsonpath-ng = ">=1.5.3" jsonschema = ">=4.16.0" packaging = ">=23.1" pendulum = ">=2.1.0,<4" -PyJWT = ">=2.4,<3.0" pytest = {version = ">=7.2.1", optional = true, markers = "extra == \"docs\" or extra == \"testing\""} pytest-durations = {version = ">=1.2.0", optional = true, markers = "extra == \"testing\""} python-dateutil = ">=2.8.2" @@ -1641,8 +1622,9 @@ typing-extensions = ">=4.5.0" urllib3 = ">=1.26,<2" [package.extras] -docs = ["furo (>=2022.12.7)", "myst-parser (>=1)", "pytest (>=7.2.1)", "sphinx (>=4.5)", "sphinx-autobuild (>=2021.3.14)", "sphinx-copybutton (>=0.3.1)", "sphinx-inline-tabs (>=2023.4.21)", "sphinx-notfound-page (>=1.0.0)", "sphinx-reredirects (>=0.1.1)"] -faker = ["faker (>=22.5,<26.0)"] +docs = ["furo (>=2024.5.6)", "myst-parser (>=3)", "pytest (>=7.2.1)", "sphinx (>=7)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinx-notfound-page (>=1.0.0)", "sphinx-reredirects (>=0.1.5)"] +faker = ["faker (>=22.5,<27.0)"] +jwt = ["PyJWT (>=2.4,<3.0)", "cryptography (>=3.4.6)"] parquet = ["numpy (>=1.22)", "numpy (>=1.22,<1.25)", "pyarrow (>=13)"] s3 = ["fs-s3fs (>=1.1.1)"] testing = ["pytest (>=7.2.1)", "pytest-durations (>=1.2.0)"] @@ -1950,4 +1932,4 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-it [metadata] lock-version = "2.0" python-versions = "<3.13,>=3.8.1" -content-hash = "84035993141a9653114c7577b1611e6b09aa51308a0e2fd4b06a2fb74cbda6f9" +content-hash = "49a89dbd1a9419440833a6ff3f88741a4946ba298b833023fab5c26c50401b5f" diff --git a/pyproject.toml b/pyproject.toml index 88b71879..3f9bd897 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ sqlalchemy = "<3" sshtunnel = "0.4.0" [tool.poetry.dependencies.singer-sdk] -version = "~=0.38.0" +version = "~=0.39.0" [tool.poetry.group.dev.dependencies] faker = ">=18.5.1" diff --git a/tap_postgres/client.py b/tap_postgres/client.py index b21e77c9..bba728e0 100644 --- a/tap_postgres/client.py +++ b/tap_postgres/client.py @@ -24,6 +24,7 @@ from singer_sdk.streams.core import REPLICATION_INCREMENTAL if TYPE_CHECKING: + from singer_sdk.helpers.types import Context from sqlalchemy.dialects import postgresql from sqlalchemy.engine import Engine from sqlalchemy.engine.reflection import Inspector @@ -269,7 +270,7 @@ def max_record_count(self) -> int | None: return self.config.get("max_record_count") # Get records from stream - def get_records(self, context: dict | None) -> t.Iterable[dict[str, t.Any]]: + def get_records(self, context: Context | None) -> t.Iterable[dict[str, t.Any]]: """Return a generator of record-type dictionary objects. If the stream has a replication_key value defined, records will be sorted by the @@ -366,7 +367,7 @@ def _increment_stream_state( self, latest_record: dict[str, Any], *, - context: dict | None = None, + context: Context | None = None, ) -> None: """Update state of stream or partition with data from the provided record. @@ -397,7 +398,7 @@ def _increment_stream_state( check_sorted=self.check_sorted, ) - def get_records(self, context: dict | None) -> Iterable[dict[str, Any]]: + def get_records(self, context: Context | None) -> Iterable[dict[str, Any]]: """Return a generator of row-type dictionary objects.""" status_interval = 5.0 # if no records in 5 seconds the tap can exit start_lsn = self.get_starting_replication_key_value(context=context) From 937bdc38b26aa318a33fe7c0fd67dfec88ceed4e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 5 Aug 2024 11:09:21 -0600 Subject: [PATCH 02/51] chore: pre-commit autoupdate (#476) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.5 → v0.5.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.5...v0.5.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index da3072e6..acc1a5c1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.5 + rev: v0.5.6 hooks: - id: ruff args: [--fix] From 0525561281d5159d622e3f46db9d59b500323057 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Aug 2024 13:05:27 +0000 Subject: [PATCH 03/51] build(deps): Bump the runtime-dependencies group with 2 updates (#479) --- poetry.lock | 108 ++++++++++++++++++++++++++-------------------------- 1 file changed, 53 insertions(+), 55 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1c27928c..600d97f1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1586,13 +1586,13 @@ files = [ [[package]] name = "singer-sdk" -version = "0.39.0" +version = "0.39.1" description = "A framework for building Singer taps" optional = false python-versions = ">=3.8" files = [ - {file = "singer_sdk-0.39.0-py3-none-any.whl", hash = "sha256:5b5aa4b485c360fb70af88c5d003b37b74c21c102adac21ea49fa023de860a23"}, - {file = "singer_sdk-0.39.0.tar.gz", hash = "sha256:e5ab6975e44324be32d15e75e86cb2d6719fc6f6d4b95ee0670a8a70c70d73bc"}, + {file = "singer_sdk-0.39.1-py3-none-any.whl", hash = "sha256:0c66709678d36f584db313f19c64c7d3b443c6879e5e476b2934918581fb213e"}, + {file = "singer_sdk-0.39.1.tar.gz", hash = "sha256:1616ac22c6917ddf2267a53e8802c10247a5e742bfb284e9dc9632ef9dc50ca4"}, ] [package.dependencies] @@ -1607,10 +1607,8 @@ joblib = 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v0.5.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.6...v0.5.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index acc1a5c1..3491cabc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.6 + rev: v0.5.7 hooks: - id: ruff args: [--fix] From d864d9c2971d7cc1f8a7a011f25b083a13e96dd9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edgar=20Ram=C3=ADrez=20Mondrag=C3=B3n?= <16805946+edgarrmondragon@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:18:45 -0600 Subject: [PATCH 06/51] feat: Bump singer-sdk to 0.40.0 (#482) --- .github/workflows/test.yml | 10 +- poetry.lock | 800 ++++++++++++++++++------------------- pyproject.toml | 7 +- 3 files changed, 409 insertions(+), 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a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.1 + rev: v0.6.2 hooks: - id: ruff args: [--fix] From ba7ad8747226a158e39ffcb898efb78d02d10e92 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edgar=20Ram=C3=ADrez=20Mondrag=C3=B3n?= <16805946+edgarrmondragon@users.noreply.github.com> Date: Mon, 26 Aug 2024 14:15:32 -0600 Subject: [PATCH 12/51] ci: Only run tests when relevant code changes (#489) --- .github/workflows/test.yml | 23 +++++++++++++++++++++++ pyproject.toml | 3 +++ 2 files changed, 26 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8900fe27..a8eb9140 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -2,9 +2,32 @@ name: Test tap-postgres on: pull_request: + branches: [main] types: [opened, synchronize, reopened] + paths: + - .github/workflows/test.yml + - log_based/** + - pagila/** + - ssh_tunnel/** + - ssl/** + - tap_postgres/** + - tests/** + - poetry.lock + - pyproject.toml + - tox.ini push: branches: [main] + paths: + - .github/workflows/test.yml + - log_based/** + - pagila/** + - ssh_tunnel/** + - ssl/** + - tap_postgres/** + - tests/** + - poetry.lock + - pyproject.toml + - tox.ini workflow_dispatch: inputs: {} diff --git a/pyproject.toml b/pyproject.toml index ac83d676..252b4644 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -121,3 +121,6 @@ sqlalchemy = "sa" [tool.ruff.lint.pydocstyle] convention = "google" + +[tool.pytest.ini_options] +addopts = '--durations=10' From c68b98c241f5d0db693c6669e8ce803af968b332 Mon Sep 17 00:00:00 2001 From: Hudo Assenco Date: Tue, 27 Aug 2024 22:46:57 -0300 Subject: [PATCH 13/51] fix: use psycopg text array decoding in wal2json messages (#490) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Slack thread: https://meltano.slack.com/archives/C06A1MD6A6L/p1724619858505739 When using log based replication, the wal2json output for columns of array types returns a string encoded in sql format. Ex: '{a,b}' The records produced by the tap in this sutation fails the target schema validation, since the schema is of type array and the value is a string. I included a test case for it. Please feel free to modify the PR, I am by no means a python developer. Related: - https://github.com/eulerto/wal2json/issues/221#issuecomment-1025143441 --------- Co-authored-by: Edgar Ramírez Mondragón <16805946+edgarrmondragon@users.noreply.github.com> --- tap_postgres/client.py | 17 ++++++++++---- tests/test_log_based.py | 52 ++++++++++++++++++++++++++++++++++++++++- 2 files changed, 64 insertions(+), 5 deletions(-) diff --git a/tap_postgres/client.py b/tap_postgres/client.py index bba728e0..2babaf53 100644 --- a/tap_postgres/client.py +++ b/tap_postgres/client.py @@ -429,7 +429,7 @@ def get_records(self, context: Context | None) -> Iterable[dict[str, Any]]: while True: message = logical_replication_cursor.read_message() if message: - row = self.consume(message) + row = self.consume(message, logical_replication_cursor) if row: yield row else: @@ -456,7 +456,7 @@ def get_records(self, context: Context | None) -> Iterable[dict[str, Any]]: logical_replication_cursor.close() logical_replication_connection.close() - def consume(self, message) -> dict | None: + def consume(self, message, cursor) -> dict | None: """Ingest WAL message.""" try: message_payload = json.loads(message.payload) @@ -476,12 +476,12 @@ def consume(self, message) -> dict | None: if message_payload["action"] in upsert_actions: for column in message_payload["columns"]: - row.update({column["name"]: column["value"]}) + row.update({column["name"]: self._parse_column_value(column, cursor)}) row.update({"_sdc_deleted_at": None}) row.update({"_sdc_lsn": message.data_start}) elif message_payload["action"] in delete_actions: for column in message_payload["identity"]: - row.update({column["name"]: column["value"]}) + row.update({column["name"]: self._parse_column_value(column, cursor)}) row.update( { "_sdc_deleted_at": datetime.datetime.utcnow().strftime( @@ -517,6 +517,15 @@ def consume(self, message) -> dict | None: return row + def _parse_column_value(self, column, cursor): + # When using log based replication, the wal2json output for columns of + # array types returns a string encoded in sql format, e.g. '{a,b}' + # https://github.com/eulerto/wal2json/issues/221#issuecomment-1025143441 + if column["type"] == "text[]": + return psycopg2.extensions.STRINGARRAY(column["value"], cursor) + + return column["value"] + def logical_replication_connection(self): """A logical replication connection to the database. diff --git a/tests/test_log_based.py b/tests/test_log_based.py index 51075a7e..5656b08e 100644 --- a/tests/test_log_based.py +++ b/tests/test_log_based.py @@ -1,7 +1,7 @@ import json import sqlalchemy as sa -from sqlalchemy.dialects.postgresql import BIGINT, TEXT +from sqlalchemy.dialects.postgresql import ARRAY, BIGINT, TEXT from tap_postgres.tap import TapPostgres from tests.test_core import PostgresTestRunner @@ -57,3 +57,53 @@ def test_null_append(): tap_class=TapPostgres, config=LOG_BASED_CONFIG, catalog=tap_catalog ) test_runner.sync_all() + + +def test_string_array_column(): + """LOG_BASED syncs failed with array columns. + + This test checks that even when a catalog contains properties with types represented + as arrays (ex: "text[]") LOG_BASED replication can properly decode their value. + """ + table_name = "test_array_column" + engine = sa.create_engine( + "postgresql://postgres:postgres@localhost:5434/postgres", future=True + ) + + metadata_obj = sa.MetaData() + table = sa.Table( + table_name, + metadata_obj, + sa.Column("id", BIGINT, primary_key=True), + sa.Column("data", ARRAY(TEXT), nullable=True), + ) + with engine.begin() as conn: + table.drop(conn, checkfirst=True) + metadata_obj.create_all(conn) + insert = table.insert().values(id=123, data=["1", "2"]) + conn.execute(insert) + insert = table.insert().values(id=321, data=['This is a "test"', "2"]) + conn.execute(insert) + + tap = TapPostgres(config=LOG_BASED_CONFIG) + tap_catalog = json.loads(tap.catalog_json_text) + altered_table_name = f"public-{table_name}" + + for stream in tap_catalog["streams"]: + if stream.get("stream") and altered_table_name not in stream["stream"]: + for metadata in stream["metadata"]: + metadata["metadata"]["selected"] = False + else: + stream["replication_method"] = "LOG_BASED" + stream["replication_key"] = "_sdc_lsn" + for metadata in stream["metadata"]: + metadata["metadata"]["selected"] = True + if metadata["breadcrumb"] == []: + metadata["metadata"]["replication-method"] = "LOG_BASED" + + test_runner = PostgresTestRunner( + tap_class=TapPostgres, config=LOG_BASED_CONFIG, catalog=tap_catalog + ) + test_runner.sync_all() + assert test_runner.record_messages[0]["record"]["data"] == ["1", "2"] + assert test_runner.record_messages[1]["record"]["data"] == ['This is a "test"', "2"] From 4146ec568ecbe124f4b0c1ca5fcba3604af94217 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Sep 2024 12:11:30 +0000 Subject: [PATCH 14/51] build(deps): Bump pypa/gh-action-pypi-publish from 1.9.0 to 1.10.0 in the actions group (#492) --- .github/workflows/release.yml | 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insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 549dcf36..3b8bee15 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.3 + rev: v0.6.4 hooks: - id: ruff args: [--fix] From b553a3221fde28d132e3f3ec831d0bfe8787f8ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edgar=20Ram=C3=ADrez=20Mondrag=C3=B3n?= <16805946+edgarrmondragon@users.noreply.github.com> Date: Mon, 9 Sep 2024 13:19:31 -0600 Subject: [PATCH 23/51] chore: Update PyPI metadata (#501) --- .github/workflows/release.yml | 2 ++ poetry.lock | 36 +++++++++++++++++------------------ pyproject.toml | 3 ++- 3 files changed, 22 insertions(+), 19 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index dd32b787..79a3047a 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -42,3 +42,5 @@ jobs: 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Contributors "] license = "MIT" readme = "README.md" homepage = "https://meltano.com" -repository = "https://github.com/meltanolabs/tap-postgres" -documentation = "https://github.com/meltanolabs/tap-postgres/blob/main/README.md" +repository = "https://github.com/MeltanoLabs/tap-postgres" +documentation = "https://github.com/MeltanoLabs/tap-postgres/blob/main/README.md" keywords = [ "Postgres", "Singer", From dfd1c46e37ca7fc1b19efd1012cbf75ea81e0e87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edgar=20Ram=C3=ADrez=20Mondrag=C3=B3n?= <16805946+edgarrmondragon@users.noreply.github.com> Date: Wed, 11 Sep 2024 12:20:29 -0600 Subject: [PATCH 25/51] chore: Do not use pendulum in tests (#505) --- poetry.lock | 288 ++++++++++------------------------ pyproject.toml | 1 - tests/test_core.py | 5 +- tests/test_replication_key.py | 12 +- 4 files changed, 88 insertions(+), 218 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1646e3d3..a1cb1b10 100644 --- a/poetry.lock +++ b/poetry.lock @@ -81,34 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"38c922d964524bbce1fc5c028c0c0498632c93d2f1160e12f91878c4ab780c0d" +content-hash = "870e0fc0e2cd8772fe03713b9646b8a86e2ad21a92c74ee2efe3bb4701400f50" diff --git a/pyproject.toml b/pyproject.toml index 1f1cbbbb..5d2d1ad3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,7 @@ sqlalchemy = "<3" sshtunnel = "0.4.0" [tool.poetry.dependencies.singer-sdk] -version = "~=0.40.0a1" +version = "~=0.41.0" extras = ["faker"] [tool.poetry.group.dev.dependencies] diff --git a/tap_postgres/client.py b/tap_postgres/client.py index 2babaf53..40e2f4b4 100644 --- a/tap_postgres/client.py +++ b/tap_postgres/client.py @@ -6,6 +6,7 @@ from __future__ import annotations import datetime +import functools import json import select import typing as t @@ -16,19 +17,59 @@ import psycopg2 import singer_sdk.helpers._typing import sqlalchemy as sa +import sqlalchemy.types from psycopg2 import extras from singer_sdk import SQLConnector, SQLStream -from singer_sdk import typing as th +from singer_sdk.connectors.sql import SQLToJSONSchema from singer_sdk.helpers._state import increment_state from singer_sdk.helpers._typing import TypeConformanceLevel from singer_sdk.streams.core import REPLICATION_INCREMENTAL +from sqlalchemy.dialects import postgresql if TYPE_CHECKING: from singer_sdk.helpers.types import Context from sqlalchemy.dialects import postgresql from sqlalchemy.engine import Engine from sqlalchemy.engine.reflection import Inspector - from sqlalchemy.types import TypeEngine + + +class PostgresSQLToJSONSchema(SQLToJSONSchema): + """Custom SQL to JSON Schema conversion for Postgres.""" + + def __init__(self, dates_as_string: bool, *args, **kwargs): + """Initialize the SQL to JSON Schema converter.""" + super().__init__(*args, **kwargs) + self.dates_as_string = dates_as_string + + @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] + def array_to_jsonschema(self, column_type: postgresql.ARRAY) -> dict: + """Override the default mapping for NUMERIC columns. + + For example, a scale of 4 translates to a multipleOf 0.0001. + """ + return { + "type": "array", + "items": self.to_jsonschema(column_type.item_type), + } + + @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] + def json_to_jsonschema(self, column_type: postgresql.JSON) -> dict: + """Override the default mapping for JSON and JSONB columns.""" + return {"type": ["string", "number", "integer", "array", "object", "boolean"]} + + @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] + def datetime_to_jsonschema(self, column_type: sqlalchemy.types.DateTime) -> dict: + """Override the default mapping for DATETIME columns.""" + if self.dates_as_string: + return {"type": ["string", "null"]} + return super().datetime_to_jsonschema(column_type) + + @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] + def date_to_jsonschema(self, column_type: sqlalchemy.types.Date) -> dict: + """Override the default mapping for DATE columns.""" + if self.dates_as_string: + return {"type": ["string", "null"]} + return super().date_to_jsonschema(column_type) def patched_conform( @@ -115,131 +156,10 @@ def __init__( super().__init__(config=config, sqlalchemy_url=sqlalchemy_url) - # Note super is static, we can get away with this because this is called once - # and is luckily referenced via the instance of the class - def to_jsonschema_type( # type: ignore[override] - self, - sql_type: str | TypeEngine | type[TypeEngine] | postgresql.ARRAY | Any, - ) -> dict: - """Return a JSON Schema representation of the provided type. - - Overridden from SQLConnector to correctly handle JSONB and Arrays. - - Also Overridden in order to call our instance method `sdk_typing_object()` - instead of the static version - - By default will call `typing.to_jsonschema_type()` for strings and SQLAlchemy - types. - - Args: - sql_type: The string representation of the SQL type, a SQLAlchemy - TypeEngine class or object, or a custom-specified object. - - Raises: - ValueError: If the type received could not be translated to jsonschema. - - Returns: - The JSON Schema representation of the provided type. - - """ - type_name = None - if isinstance(sql_type, str): - type_name = sql_type - elif isinstance(sql_type, sa.types.TypeEngine): - type_name = type(sql_type).__name__ - - if ( - type_name is not None - and isinstance(sql_type, sa.dialects.postgresql.ARRAY) - and type_name == "ARRAY" - ): - array_type = self.sdk_typing_object(sql_type.item_type) - return th.ArrayType(array_type).type_dict - return self.sdk_typing_object(sql_type).type_dict - - def sdk_typing_object( - self, - from_type: str | TypeEngine | type[TypeEngine], - ) -> ( - th.DateTimeType - | th.NumberType - | th.IntegerType - | th.DateType - | th.StringType - | th.BooleanType - | th.CustomType - ): - """Return the JSON Schema dict that describes the sql type. - - Args: - from_type: The SQL type as a string or as a TypeEngine. If a TypeEngine is - provided, it may be provided as a class or a specific object instance. - - Raises: - ValueError: If the `from_type` value is not of type `str` or `TypeEngine`. - - Returns: - A compatible JSON Schema type definition. - """ - # NOTE: This is an ordered mapping, with earlier mappings taking precedence. If - # the SQL-provided type contains the type name on the left, the mapping will - # return the respective singer type. - # NOTE: jsonb and json should theoretically be th.AnyType().type_dict but that - # causes problems down the line with an error like: - # singer_sdk.helpers._typing.EmptySchemaTypeError: Could not detect type from - # empty type_dict. Did you forget to define a property in the stream schema? - sqltype_lookup: dict[ - str, - th.DateTimeType - | th.NumberType - | th.IntegerType - | th.DateType - | th.StringType - | th.BooleanType - | th.CustomType, - ] = { - "jsonb": th.CustomType( - {"type": ["string", "number", "integer", "array", "object", "boolean"]} - ), - "json": th.CustomType( - {"type": ["string", "number", "integer", "array", "object", "boolean"]} - ), - "timestamp": th.DateTimeType(), - "datetime": th.DateTimeType(), - "date": th.DateType(), - "int": th.IntegerType(), - "numeric": th.NumberType(), - "decimal": th.NumberType(), - "double": th.NumberType(), - "float": th.NumberType(), - "real": th.NumberType(), - "float4": th.NumberType(), - "string": th.StringType(), - "text": th.StringType(), - "char": th.StringType(), - "bool": th.BooleanType(), - "variant": th.StringType(), - } - if self.config["dates_as_string"] is True: - sqltype_lookup["date"] = th.StringType() - sqltype_lookup["datetime"] = th.StringType() - if isinstance(from_type, str): - type_name = from_type - elif isinstance(from_type, sa.types.TypeEngine): - type_name = type(from_type).__name__ - elif isinstance(from_type, type) and issubclass(from_type, sa.types.TypeEngine): - type_name = from_type.__name__ - else: - raise ValueError( - "Expected `str` or a SQLAlchemy `TypeEngine` object or type." - ) - - # Look for the type name within the known SQL type names: - for sqltype, jsonschema_type in sqltype_lookup.items(): - if sqltype.lower() in type_name.lower(): - return jsonschema_type - - return sqltype_lookup["string"] # safe failover to str + @functools.cached_property + def sql_to_jsonschema(self): + """Return a mapping of SQL types to JSON Schema types.""" + return PostgresSQLToJSONSchema(dates_as_string=self.config["dates_as_string"]) def get_schema_names(self, engine: Engine, inspected: Inspector) -> list[str]: """Return a list of schema names in DB, or overrides with user-provided values. 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a/.github/workflows/constraints.txt b/.github/workflows/constraints.txt index 85cdce66..162b323f 100644 --- a/.github/workflows/constraints.txt +++ b/.github/workflows/constraints.txt @@ -1,2 +1,2 @@ -pip==24.2 +pip==24.3.1 poetry==1.8.4 From aaa3b7e60e0c5c85b8ca3d98917ca92a759f4c7e Mon Sep 17 00:00:00 2001 From: Derek Visch Date: Mon, 28 Oct 2024 10:19:48 -0400 Subject: [PATCH 45/51] chore: Remove visch from Dependabot (#525) I don't do any of there anyway! --- .github/dependabot.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index aff72c86..1752835e 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -11,8 +11,6 @@ updates: interval: weekly timezone: "America/New_York" time: "07:23" - reviewers: - - "visch" versioning-strategy: increase-if-necessary groups: development-dependencies: @@ -39,8 +37,6 @@ updates: interval: weekly timezone: "America/New_York" time: "07:23" - reviewers: - - "visch" groups: actions: patterns: From 6efa7d0c7aeefaa2f2d1f82126a6e9ffa7ee23f3 Mon Sep 17 00:00:00 2001 From: Jon Cass Date: Fri, 1 Nov 2024 10:33:51 -0400 Subject: [PATCH 46/51] feat: Add json_as_object option (#526) To allow JSON and JSONB to be tapped as plain objects See [this Slack thread](https://meltano.slack.com/archives/C069CQNHDNF/p1729784981090099) for context --- README.md | 3 ++ tap_postgres/client.py | 10 ++++-- tap_postgres/tap.py | 8 +++++ tests/test_core.py | 73 ++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 92 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 69bedbc8..e6f6d076 100644 --- a/README.md +++ b/README.md @@ -26,6 +26,7 @@ Built with the [Meltano Singer SDK](https://sdk.meltano.com). | sqlalchemy_url | False | None | Example postgresql://[username]:[password]@localhost:5432/[db_name] | | filter_schemas | False | None | If an array of schema names is provided, the tap will only process the specified Postgres schemas and ignore others. If left blank, the tap automatically determines ALL available Postgres schemas. | | dates_as_string | False | 0 | Defaults to false, if true, date, and timestamp fields will be Strings. If you see ValueError: Year is out of range, try setting this to True. | +| json_as_object | False | 0 | Defaults to false, if true, json and jsonb fields will be Objects. | | ssh_tunnel | False | None | SSH Tunnel Configuration, this is a json object | | ssh_tunnel.enable | False | 0 | Enable an ssh tunnel (also known as bastion server), see the other ssh_tunnel.* properties for more details | | ssh_tunnel.host | False | None | Host of the bastion server, this is the host we'll connect to via ssh | @@ -132,6 +133,8 @@ Create tests within the `tap_postgres/tests` subfolder and poetry run pytest ``` +NOTE: Running the tests requires a locally running postgres. See tests/settings.py for the expected configuration. + You can also test the `tap-postgres` CLI interface directly using `poetry run`: ```bash diff --git a/tap_postgres/client.py b/tap_postgres/client.py index 40e2f4b4..f3ceecfa 100644 --- a/tap_postgres/client.py +++ b/tap_postgres/client.py @@ -36,10 +36,11 @@ class PostgresSQLToJSONSchema(SQLToJSONSchema): """Custom SQL to JSON Schema conversion for Postgres.""" - def __init__(self, dates_as_string: bool, *args, **kwargs): + def __init__(self, dates_as_string: bool, json_as_object: bool, *args, **kwargs): """Initialize the SQL to JSON Schema converter.""" super().__init__(*args, **kwargs) self.dates_as_string = dates_as_string + self.json_as_object = json_as_object @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] def array_to_jsonschema(self, column_type: postgresql.ARRAY) -> dict: @@ -55,6 +56,8 @@ def array_to_jsonschema(self, column_type: postgresql.ARRAY) -> dict: @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] def json_to_jsonschema(self, column_type: postgresql.JSON) -> dict: """Override the default mapping for JSON and JSONB columns.""" + if self.json_as_object: + return {"type": ["object", "null"]} return {"type": ["string", "number", "integer", "array", "object", "boolean"]} @SQLToJSONSchema.to_jsonschema.register # type: ignore[attr-defined] @@ -159,7 +162,10 @@ def __init__( @functools.cached_property def sql_to_jsonschema(self): """Return a mapping of SQL types to JSON Schema types.""" - return PostgresSQLToJSONSchema(dates_as_string=self.config["dates_as_string"]) + return PostgresSQLToJSONSchema( + dates_as_string=self.config["dates_as_string"], + json_as_object=self.config["json_as_object"], + ) def get_schema_names(self, engine: Engine, inspected: Inspector) -> list[str]: """Return a list of schema names in DB, or overrides with user-provided values. diff --git a/tap_postgres/tap.py b/tap_postgres/tap.py index ed75a470..31831c5e 100644 --- a/tap_postgres/tap.py +++ b/tap_postgres/tap.py @@ -176,6 +176,14 @@ def __init__( ), default=False, ), + th.Property( + "json_as_object", + th.BooleanType, + description=( + "Defaults to false, if true, json and jsonb fields will be Objects." + ), + default=False, + ), th.Property( "ssh_tunnel", th.ObjectType( diff --git a/tests/test_core.py b/tests/test_core.py index 0c29b246..32884668 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -338,6 +338,79 @@ def test_jsonb_array(): assert test_runner.records[altered_table_name][i] == rows[i] +def test_json_as_object(): + """Some use cases require JSON and JSONB columns to be typed as Objects.""" + table_name = "test_json_as_object" + engine = sa.create_engine(SAMPLE_CONFIG["sqlalchemy_url"], future=True) + + metadata_obj = sa.MetaData() + table = sa.Table( + table_name, + metadata_obj, + sa.Column("column_jsonb", JSONB), + sa.Column("column_json", JSON), + ) + + rows = [ + {"column_jsonb": {"foo": "bar"}, "column_json": {"baz": "foo"}}, + {"column_jsonb": 3.14, "column_json": -9.3}, + {"column_jsonb": 22, "column_json": 10000000}, + {"column_jsonb": {}, "column_json": {}}, + {"column_jsonb": ["bar", "foo"], "column_json": ["foo", "baz"]}, + {"column_jsonb": True, "column_json": False}, + ] + + with engine.begin() as conn: + table.drop(conn, checkfirst=True) + metadata_obj.create_all(conn) + insert = table.insert().values(rows) + conn.execute(insert) + + copied_config = copy.deepcopy(SAMPLE_CONFIG) + # This should cause the same data to pass + copied_config["json_as_object"] = True + + tap = TapPostgres(config=copied_config) + tap_catalog = json.loads(tap.catalog_json_text) + altered_table_name = f"{DB_SCHEMA_NAME}-{table_name}" + + for stream in tap_catalog["streams"]: + if stream.get("stream") and altered_table_name not in stream["stream"]: + for metadata in stream["metadata"]: + metadata["metadata"]["selected"] = False + else: + for metadata in stream["metadata"]: + metadata["metadata"]["selected"] = True + if metadata["breadcrumb"] == []: + metadata["metadata"]["replication-method"] = "FULL_TABLE" + + test_runner = PostgresTestRunner( + tap_class=TapPostgres, config=SAMPLE_CONFIG, catalog=tap_catalog + ) + test_runner.sync_all() + for schema_message in test_runner.schema_messages: + if ( + "stream" in schema_message + and schema_message["stream"] == altered_table_name + ): + assert schema_message["schema"]["properties"]["column_jsonb"] == { + "type": [ + "object", + "null", + ] + } + assert schema_message["schema"]["properties"]["column_json"] == { + "type": [ + "object", + "null", + ] + } + + assert len(rows) == len(test_runner.records[altered_table_name]) + for expected_row, actual_row in zip(rows, test_runner.records[altered_table_name]): + assert actual_row == expected_row + + def test_numeric_types(): """Schema was wrong for Decimal objects. 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rev: v0.6.9 + rev: v0.7.2 hooks: - id: ruff args: [--fix] From b550f86f115716017bc09fcd9b3cebddfc9a40b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edgar=20Ram=C3=ADrez=20Mondrag=C3=B3n?= <16805946+edgarrmondragon@users.noreply.github.com> Date: Mon, 4 Nov 2024 11:31:35 -0600 Subject: [PATCH 50/51] chore: Start testing with Postgres 12-17 and Python 3.13, dropped support for Python 3.8 (#531) Related: - Closes https://github.com/MeltanoLabs/tap-postgres/issues/527 --- .github/workflows/constraints.txt | 1 + .github/workflows/test.yml | 47 ++- .gitignore | 27 ++ Dockerfile | 27 +- README.md | 4 + docker-compose.yml | 6 +- poetry.lock | 532 +++++++++++++++--------------- pyproject.toml | 11 +- tap_postgres/client.py | 4 +- tap_postgres/tap.py | 4 +- tox.ini | 37 ++- 11 files changed, 382 insertions(+), 318 deletions(-) diff --git a/.github/workflows/constraints.txt b/.github/workflows/constraints.txt index 162b323f..83184a86 100644 --- a/.github/workflows/constraints.txt +++ b/.github/workflows/constraints.txt @@ -1,2 +1,3 @@ pip==24.3.1 poetry==1.8.4 +tox==4.23.2 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8a89c18f..81f3e5d7 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -1,5 +1,8 @@ name: Test tap-postgres +env: + FORCE_COLOR: 1 + on: pull_request: branches: [main] @@ -37,6 +40,7 @@ concurrency: jobs: tests: + name: Python ${{ matrix.python-version }} / Postgres ${{ matrix.postgres-version }} runs-on: ubuntu-latest env: PIP_CONSTRAINT: ${{ github.workspace }}/.github/workflows/constraints.txt @@ -44,11 +48,24 @@ jobs: fail-fast: false matrix: python-version: + - "3.13" - "3.12" - "3.11" - "3.10" - "3.9" - - "3.8" + postgres-version: + - "17" + include: + - python-version: "3.13" + postgres-version: "12" + - python-version: "3.13" + postgres-version: "13" + - python-version: "3.13" + postgres-version: "14" + - python-version: "3.13" + postgres-version: "15" + - python-version: "3.13" + postgres-version: "16" steps: - name: Checkout code @@ -62,13 +79,19 @@ jobs: chmod 600 ssl/pkey.key - name: Build Postgres container + env: + POSTGRES_VERSION: ${{ matrix.postgres-version }} run: | - docker build . --tag meltano/log_based + docker build . --build-arg POSTGRES_VERSION=${POSTGRES_VERSION} --tag meltano/log_based - name: Compose Postgres container + env: + POSTGRES_VERSION: ${{ matrix.postgres-version }} run: | docker compose -f docker-compose.yml up -d --wait --wait-timeout=30 - uses: isbang/compose-action@v2.0.2 + env: + POSTGRES_VERSION: ${{ matrix.postgres-version }} # Leaving comments as this makes testing the openssh docker image easier and should save someone some time later # - name: Test SSH File Permissiosn @@ -78,27 +101,21 @@ jobs: # docker exec openssh-server ps aux + - run: docker ps + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} allow-prereleases: true - - name: Upgrade pip - run: | - pip install pip - pip --version - - name: Install Poetry - run: | - pip install poetry - poetry --version - - name: Install dependencies + - name: Install Tox run: | - poetry env use python${{ matrix.python-version }} - poetry install + python -m pip install --upgrade pip + pipx install tox - name: Run pytest run: | - poetry run pytest + tox -e $(echo py${{ matrix.python-version }} | tr -d .) - name: Run lint run: | - poetry run tox -e lint + tox -e lint diff --git a/.gitignore b/.gitignore index 2a915d9c..a6714792 100644 --- a/.gitignore +++ b/.gitignore @@ -136,3 +136,30 @@ dmypy.json # Pyre type checker .pyre/ + +# General +.DS_Store +.AppleDouble +.LSOverride + +# Icon must end with two \r +Icon + +# Thumbnails +._* + +# Files that might appear in the root of a volume +.DocumentRevisions-V100 +.fseventsd +.Spotlight-V100 +.TemporaryItems +.Trashes +.VolumeIcon.icns +.com.apple.timemachine.donotpresent + +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk diff --git a/Dockerfile b/Dockerfile index 478adf97..e5e8cdfc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,12 +1,17 @@ -FROM postgres:16 +ARG POSTGRES_VERSION=17 +FROM postgres:${POSTGRES_VERSION} -RUN apt-get update -RUN apt-mark hold locales -RUN apt-get install curl ca-certificates -y -RUN install -d /usr/share/postgresql-common/pgdg -RUN curl -o /usr/share/postgresql-common/pgdg/apt.postgresql.org.asc --fail https://www.postgresql.org/media/keys/ACCC4CF8.asc -RUN sh -c 'echo "deb [signed-by=/usr/share/postgresql-common/pgdg/apt.postgresql.org.asc] https://apt.postgresql.org/pub/repos/apt bookworm-pgdg main" > /etc/apt/sources.list.d/pgdg.list' -RUN apt-get update -RUN apt-get install postgresql-server-dev-16 -y -RUN sh -c 'export PATH=/usr/lib/postgresql/16/bin:$PATH' -RUN apt-get install postgresql-16-wal2json -y +ARG POSTGRES_VERSION=17 + +# Install prerequisites and configure PostgreSQL for wal2json +RUN apt-get update && apt-mark hold locales && \ + apt-get install -y curl ca-certificates && \ + install -d /usr/share/postgresql-common/pgdg && \ + curl -o /usr/share/postgresql-common/pgdg/apt.postgresql.org.asc --fail https://www.postgresql.org/media/keys/ACCC4CF8.asc && \ + sh -c 'echo "deb [signed-by=/usr/share/postgresql-common/pgdg/apt.postgresql.org.asc] https://apt.postgresql.org/pub/repos/apt bookworm-pgdg main" > /etc/apt/sources.list.d/pgdg.list' + +RUN echo "Setting up PostgreSQL ${POSTGRES_VERSION} with wal2json" && \ + apt-get update && \ + apt-get install -y postgresql-server-dev-${POSTGRES_VERSION} && \ + export PATH=/usr/lib/postgresql/${POSTGRES_VERSION}/bin:$PATH && \ + apt-get install -y postgresql-${POSTGRES_VERSION}-wal2json diff --git a/README.md b/README.md index e6f6d076..a62c6f6c 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,10 @@ Built with the [Meltano Singer SDK](https://sdk.meltano.com). * `stream-maps` * `schema-flattening` +## Supported Python and PostgreSQL Versions + +This tap is tested with all actively supported [Python](https://devguide.python.org/versions/#supported-versions) and [PostgreSQL](https://www.postgresql.org/support/versioning/) versions. At the time of writing, this includes Python 3.9 through 3.13 and PostgreSQL 12 through 17. + ## Settings | Setting | Required | Default | Description | diff --git a/docker-compose.yml b/docker-compose.yml index df081c77..f3ed492c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,7 +21,7 @@ services: - inner postgres_no_ssl: - image: postgres:latest + image: postgres:${POSTGRES_VERSION:-latest} environment: POSTGRES_USER: postgres POSTGRES_PASSWORD: postgres @@ -30,7 +30,7 @@ services: - "5432:5432" postgresdb: - image: postgres:13.0 + image: postgres:${POSTGRES_VERSION:-latest} environment: POSTGRES_USER: postgres POSTGRES_PASSWORD: postgres @@ -40,7 +40,7 @@ services: ipv4_address: 10.5.0.5 postgres_ssl: - image: postgres:16 + image: postgres:${POSTGRES_VERSION:-latest} command: postgres -c ssl=on -c ssl_cert_file=/var/lib/postgresql/server.crt -c ssl_key_file=/var/lib/postgresql/server.key -c ssl_ca_file=/var/lib/postgresql/ca.crt -c hba_file=/var/lib/postgresql/pg_hba.conf environment: POSTGRES_USER: postgres diff --git a/poetry.lock b/poetry.lock index 560e5d0a..cf45318c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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License", "Operating System :: OS Independent", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Programming Language :: Python :: Implementation :: CPython", ] packages = [ @@ -33,7 +33,7 @@ packages = [ [tool.poetry.dependencies] -python = ">=3.8.1" +python = ">=3.9" psycopg2-binary = "2.9.10" sqlalchemy = "<3" sshtunnel = "0.4.0" @@ -61,7 +61,7 @@ extras = ["testing"] [tool.mypy] exclude = "tests" -python_version = "3.12" +python_version = "3.13" warn_unused_configs = true warn_unused_ignores = true @@ -73,8 +73,8 @@ module = [ [build-system] requires = [ - "poetry-core==1.9.0", - "poetry-dynamic-versioning==1.4.0", + "poetry-core==1.9.1", + "poetry-dynamic-versioning==1.4.1", ] build-backend = "poetry_dynamic_versioning.backend" @@ -88,6 +88,7 @@ vcs = "git" style = "pep440" [tool.ruff] +target-version = "py39" [tool.ruff.lint] select = [ diff --git a/tap_postgres/client.py b/tap_postgres/client.py index f3ceecfa..a6ae564c 100644 --- a/tap_postgres/client.py +++ b/tap_postgres/client.py @@ -12,7 +12,7 @@ import typing as t from functools import cached_property from types import MappingProxyType -from typing import TYPE_CHECKING, Any, Iterable, Mapping +from typing import TYPE_CHECKING, Any import psycopg2 import singer_sdk.helpers._typing @@ -27,6 +27,8 @@ from sqlalchemy.dialects import postgresql if TYPE_CHECKING: + from collections.abc import Iterable, Mapping + from singer_sdk.helpers.types import Context from sqlalchemy.dialects import postgresql from sqlalchemy.engine import Engine diff --git a/tap_postgres/tap.py b/tap_postgres/tap.py index 31831c5e..c3fc6ce3 100644 --- a/tap_postgres/tap.py +++ b/tap_postgres/tap.py @@ -9,7 +9,7 @@ import sys from functools import cached_property from os import chmod, path -from typing import TYPE_CHECKING, Any, Sequence, cast +from typing import TYPE_CHECKING, Any, cast import paramiko from singer_sdk import SQLStream, SQLTap, Stream @@ -30,7 +30,7 @@ ) if TYPE_CHECKING: - from collections.abc import Mapping + from collections.abc import Mapping, Sequence class TapPostgres(SQLTap): diff --git a/tox.ini b/tox.ini index 03314926..bc71e5f7 100644 --- a/tox.ini +++ b/tox.ini @@ -1,34 +1,41 @@ # This file can be used to customize tox tests as well as other test frameworks like flake8 and mypy [tox] -envlist = py38 -; envlist = py37, py38, py39 +envlist = py313 isolated_build = true +min_version = 4 [testenv] -allowlist_externals = poetry - -[testenv:pytest] # Run the python tests. # To execute, run `tox -e pytest` -envlist = py38, py39, py310, py311, py312 +envlist = py3{9,10,11,12,13} +deps = + pytest commands = - poetry install -v - poetry run pytest + pytest [testenv:format] # Attempt to auto-resolve lint errors before they are raised. # To execute, run `tox -e format` +skip_install = true +deps = + ruff commands = - poetry install -v - poetry run ruff check --fix tap_postgres/ - poetry run ruff format tap_postgres/ + ruff check tap_postgres/ + ruff format tap_postgres/ [testenv:lint] # Raise an error if lint and style standards are not met. # To execute, run `tox -e lint` +deps = + mypy + ruff + types-paramiko + types-simplejson + types-sqlalchemy + types-jsonschema + types-psycopg2 commands = - poetry install -v - poetry run ruff check --diff tap_postgres/ - poetry run ruff format --check tap_postgres/ - poetry run mypy . + ruff check --diff tap_postgres/ + ruff format --check tap_postgres/ + mypy . From 9bb40d155bc2f04142043ec276c3492b68339b38 Mon Sep 17 00:00:00 2001 From: James Meneghello Date: Wed, 6 Nov 2024 07:30:03 +0800 Subject: [PATCH 51/51] refactor: Optimise metadata discovery for large databases (#528) Overrides the SDK functions to instead use the `get_multi_*` functions from SQLAlchemy Inspector. On our database of ~120 tables, this reduces the discovery runtime from 10-12 minutes to about 30 seconds. - Closes #284 --- tap_postgres/client.py | 137 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 137 insertions(+) diff --git a/tap_postgres/client.py b/tap_postgres/client.py index a6ae564c..42c3ef9f 100644 --- a/tap_postgres/client.py +++ b/tap_postgres/client.py @@ -20,6 +20,8 @@ import sqlalchemy.types from psycopg2 import extras from singer_sdk import SQLConnector, SQLStream +from singer_sdk import typing as th +from singer_sdk._singerlib import CatalogEntry, MetadataMapping, Schema from singer_sdk.connectors.sql import SQLToJSONSchema from singer_sdk.helpers._state import increment_state from singer_sdk.helpers._typing import TypeConformanceLevel @@ -32,6 +34,12 @@ from singer_sdk.helpers.types import Context from sqlalchemy.dialects import postgresql from sqlalchemy.engine import Engine + from sqlalchemy.engine.interfaces import ( # type: ignore[attr-defined] + ReflectedColumn, + ReflectedIndex, + ReflectedPrimaryKeyConstraint, + TableKey, + ) from sqlalchemy.engine.reflection import Inspector @@ -183,6 +191,135 @@ def get_schema_names(self, engine: Engine, inspected: Inspector) -> list[str]: return self.config["filter_schemas"] return super().get_schema_names(engine, inspected) + # Uses information_schema for speed. + def discover_catalog_entry_optimized( # noqa: PLR0913 + self, + engine: Engine, + inspected: Inspector, + schema_name: str, + table_name: str, + is_view: bool, + table_data: dict[TableKey, list[ReflectedColumn]], + pk_data: dict[TableKey, ReflectedPrimaryKeyConstraint], + index_data: dict[TableKey, list[ReflectedIndex]], + ) -> CatalogEntry: + """Create `CatalogEntry` object for the given table or a view. + + Args: + engine: SQLAlchemy engine + inspected: SQLAlchemy inspector instance for engine + schema_name: Schema name to inspect + table_name: Name of the table or a view + is_view: Flag whether this object is a view, returned by `get_object_names` + table_data: Cached inspector data for the relevant tables + pk_data: Cached inspector data for the relevant primary keys + index_data: Cached inspector data for the relevant indexes + + Returns: + `CatalogEntry` object for the given table or a view + """ + # Initialize unique stream name + unique_stream_id = f"{schema_name}-{table_name}" + table_key = (schema_name, table_name) + + # Detect key properties + possible_primary_keys: list[list[str]] = [] + pk_def = pk_data.get(table_key, {}) + if pk_def and "constrained_columns" in pk_def: + possible_primary_keys.append(pk_def["constrained_columns"]) + + # An element of the columns list is ``None`` if it's an expression and is + # returned in the ``expressions`` list of the reflected index. + possible_primary_keys.extend( + index_def["column_names"] + for index_def in index_data.get(table_key, []) + if index_def.get("unique", False) + ) + + key_properties = next(iter(possible_primary_keys), None) + + # Initialize columns list + table_schema = th.PropertiesList() + for column_def in table_data.get(table_key, []): + column_name = column_def["name"] + is_nullable = column_def.get("nullable", False) + jsonschema_type: dict = self.to_jsonschema_type(column_def["type"]) + table_schema.append( + th.Property( + name=column_name, + wrapped=th.CustomType(jsonschema_type), + nullable=is_nullable, + required=column_name in key_properties if key_properties else False, + ), + ) + schema = table_schema.to_dict() + + # Initialize available replication methods + addl_replication_methods: list[str] = [""] # By default an empty list. + # Notes regarding replication methods: + # - 'INCREMENTAL' replication must be enabled by the user by specifying + # a replication_key value. + # - 'LOG_BASED' replication must be enabled by the developer, according + # to source-specific implementation capabilities. + replication_method = next(reversed(["FULL_TABLE", *addl_replication_methods])) + + # Create the catalog entry object + return CatalogEntry( + tap_stream_id=unique_stream_id, + stream=unique_stream_id, + table=table_name, + key_properties=key_properties, + schema=Schema.from_dict(schema), + is_view=is_view, + replication_method=replication_method, + metadata=MetadataMapping.get_standard_metadata( + schema_name=schema_name, + schema=schema, + replication_method=replication_method, + key_properties=key_properties, + valid_replication_keys=None, # Must be defined by user + ), + database=None, # Expects single-database context + row_count=None, + stream_alias=None, + replication_key=None, # Must be defined by user + ) + + def discover_catalog_entries(self) -> list[dict]: + """Return a list of catalog entries from discovery. + + Returns: + The discovered catalog entries as a list. + """ + result: list[dict] = [] + engine = self._engine + inspected = sa.inspect(engine) + for schema_name in self.get_schema_names(engine, inspected): + # Use get_multi_* data here instead of pulling per-table + table_data = inspected.get_multi_columns(schema=schema_name) + pk_data = inspected.get_multi_pk_constraint(schema=schema_name) + index_data = inspected.get_multi_indexes(schema=schema_name) + + # Iterate through each table and view + for table_name, is_view in self.get_object_names( + engine, + inspected, + schema_name, + ): + catalog_entry = self.discover_catalog_entry_optimized( + engine, + inspected, + schema_name, + table_name, + is_view, + table_data, + pk_data, + index_data, + ) + result.append(catalog_entry.to_dict()) + + return result + class PostgresStream(SQLStream): """Stream class for Postgres streams."""