From ec86a758f51ee0340a3ea5ca7eab54e2e5b724ad Mon Sep 17 00:00:00 2001 From: Mats Rydberg Date: Fri, 18 Oct 2024 11:34:52 +0200 Subject: [PATCH 1/8] Add retrying to batch writing MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Fixed number of retries (10) - Retries on three different flight errors Co-authored-by: Max Kießling --- src/neo4j_arrow/_client.py | 44 +++++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 20 deletions(-) diff --git a/src/neo4j_arrow/_client.py b/src/neo4j_arrow/_client.py index cf5edcc..7b94636 100644 --- a/src/neo4j_arrow/_client.py +++ b/src/neo4j_arrow/_client.py @@ -1,5 +1,5 @@ import logging -from collections import abc +import time from enum import Enum import json @@ -10,7 +10,6 @@ from .model import Graph from typing import ( - cast, Any, Callable, Dict, @@ -276,41 +275,46 @@ def _rename_and_add_column( def _write_batches( self, desc: Dict[str, Any], - batches: Union[pa.RecordBatch, Iterable[pa.RecordBatch]], + batches: List[pa.RecordBatch], mapping_fn: Optional[MappingFn] = None, ) -> Result: """ Write PyArrow RecordBatches to the GDS Flight service. """ - if isinstance(batches, abc.Iterable): - batches = iter(batches) - else: - batches = iter([batches]) + if len(batches) == 0: + raise Exception("no record batches provided") fn = mapping_fn or self._nop - - first = next(batches, None) - if not first: - raise Exception("empty iterable of record batches provided") - first = cast(pa.RecordBatch, fn(first)) + schema = fn(batches[0]).schema client = self._client() upload_descriptor = flight.FlightDescriptor.for_command(json.dumps(desc).encode("utf-8")) n_rows, n_bytes = 0, 0 try: - writer, _ = client.do_put(upload_descriptor, first.schema, self.call_opts) + writer, _ = client.do_put(upload_descriptor, schema, self.call_opts) with writer: - writer.write_batch(first) - n_rows += first.num_rows - n_bytes += first.get_total_buffer_size() - for remaining in batches: - writer.write_batch(fn(remaining)) - n_rows += remaining.num_rows - n_bytes += remaining.get_total_buffer_size() + for batch in batches: + mapped_batch = fn(batch) + self._write_batch_with_retries(mapped_batch, writer) + n_rows += batch.num_rows + n_bytes += batch.get_total_buffer_size() except Exception as e: raise error.interpret(e) return n_rows, n_bytes + def _write_batch_with_retries(self, mapped_batch, writer): + num_retries = 10 + while True: + try: + writer.write_batch(mapped_batch) + break + except flight.FlightUnavailableError | flight.FlightTimedOutError | flight.FlightInternalError as e: + self.logger.exception(f"Encountered transient error; retrying {num_retries} more times ...") + time.sleep(0.1 / num_retries) + num_retries -= 1 + if num_retries == 0: + raise e + def start( self, action: str = "CREATE_GRAPH", From a53d10b53199ac4197f1b9248fd46ed9b791bef3 Mon Sep 17 00:00:00 2001 From: Mats Rydberg Date: Fri, 18 Oct 2024 17:32:48 +0200 Subject: [PATCH 2/8] Read metadata before returning MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The ambition is to make sure to have received an ACK from the server before continuing to send a DONE message. Co-authored-by: Max Kießling --- src/neo4j_arrow/_client.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/neo4j_arrow/_client.py b/src/neo4j_arrow/_client.py index 7b94636..a6a9371 100644 --- a/src/neo4j_arrow/_client.py +++ b/src/neo4j_arrow/_client.py @@ -291,13 +291,14 @@ def _write_batches( upload_descriptor = flight.FlightDescriptor.for_command(json.dumps(desc).encode("utf-8")) n_rows, n_bytes = 0, 0 try: - writer, _ = client.do_put(upload_descriptor, schema, self.call_opts) + writer, metadata_reader = client.do_put(upload_descriptor, schema, self.call_opts) with writer: for batch in batches: mapped_batch = fn(batch) self._write_batch_with_retries(mapped_batch, writer) n_rows += batch.num_rows n_bytes += batch.get_total_buffer_size() + metadata_reader.read() except Exception as e: raise error.interpret(e) return n_rows, n_bytes From ec9db4a6e018f6b0f9ff66aab54593a874b6f68a Mon Sep 17 00:00:00 2001 From: Ali Ince Date: Mon, 21 Oct 2024 12:01:28 +0100 Subject: [PATCH 3/8] Fix numpy to <2 version and add new pyarrow versions --- poetry.lock | 931 ++++++++++++++++++++++++------------------------- pyproject.toml | 3 +- tox.ini | 9 +- 3 files changed, 461 insertions(+), 482 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7b2d926..3892ead 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,74 +2,76 @@ [[package]] name = "attrs" -version = "23.1.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - 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-content-hash = "fefe72cc41f21a05e122538766fd798ff21fa75d03f147422b6a91d45878453a" +content-hash = "83f5099d9cee7e49626c269ed81727cced4791e006bde27a3114aac184e972dd" diff --git a/pyproject.toml b/pyproject.toml index daa5bab..2da098f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,8 @@ packages = [{ include = "neo4j_arrow", from = "src" }] [tool.poetry.dependencies] python = ">=3.9, <4" -pyarrow = ">=10, <15" +pyarrow = ">=10, <18" +numpy = "<2" [tool.poetry.group.dev.dependencies] pytest = "^7.4.3" diff --git a/tox.ini b/tox.ini index 6d3fa71..c398b3d 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,5 @@ [tox] -env_list = py{39,310,311}-pyarrow{10,11,12,13,14}-unit, py{312}-pyarrow{14}-unit, py{39,310,311,312}-neo4j{4.4,5}-integration +env_list = py{39,310,311}-pyarrow{10,11,12,13,14,15,16,17}-unit, py{312}-pyarrow{14,15,16,17}-unit, py{39,310,311,312}-neo4j{4.4,5}-integration [testenv] deps = @@ -11,16 +11,19 @@ deps = pyarrow12: pyarrow >= 12.0, < 13.0 pyarrow13: pyarrow >= 13.0, < 14.0 pyarrow14: pyarrow >= 14.0, < 15.0 + pyarrow15: pyarrow >= 15.0, < 16.0 + pyarrow16: pyarrow >= 16.0, < 17.0 + pyarrow17: pyarrow >= 17.0, < 18.0 warn_args = py{39,310,311,312}: -W error commands = unit: python -m pytest {[testenv]warn_args} -v {posargs} tests/unit integration: python -m pytest -v {posargs} tests/integration -[testenv:py{39,310,311}-pyarrow{10,11,12,13,14}-unit] +[testenv:py{39,310,311}-pyarrow{10,11,12,13,14,15,16,17}-unit] labels = unit -[testenv:py{312}-pyarrow{14}-unit] +[testenv:py{312}-pyarrow{14,15,16,17}-unit] labels = unit [testenv:py{39,310,311,312}-neo4j{4.4,5}-integration] From 727b987e5db8431a08d8928b9db8eebe1a47bf41 Mon Sep 17 00:00:00 2001 From: Ali Ince Date: Mon, 21 Oct 2024 16:10:38 +0100 Subject: [PATCH 4/8] Explicitly set username and password --- tests/integration/conftest.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py index 8bb6ac2..cabbb28 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -19,6 +19,9 @@ def gds_version(driver: neo4j.Driver) -> str: @pytest.fixture(scope="module") def neo4j(): + testcontainers.neo4j.Neo4jContainer.NEO4J_USER = "neo4j" + testcontainers.neo4j.Neo4jContainer.NEO4J_ADMIN_PASSWORD = "password" + container = ( testcontainers.neo4j.Neo4jContainer(os.getenv("NEO4J_IMAGE", "neo4j:5-enterprise")) .with_volume_mapping(os.getenv("GDS_LICENSE_FILE", "/tmp/gds.license"), "/licenses/gds.license") @@ -31,6 +34,8 @@ def neo4j(): .with_env("NEO4J_gds_arrow_listen__address", "0.0.0.0") .with_exposed_ports(7687, 7474, 8491) ) + container.NEO4J_USER = "neo4j" + container.NEO4J_ADMIN_PASSWORD = "password" container.start() yield container From a56d2721cacd2ddd092d9b492545a7538670482c Mon Sep 17 00:00:00 2001 From: Ali Ince Date: Mon, 21 Oct 2024 16:16:32 +0100 Subject: [PATCH 5/8] Update poetry --- .github/workflows/build.yaml | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 9dc1dcc..f374ab3 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -25,7 +25,7 @@ jobs: - name: install poetry run: | python3 -m venv $POETRY_HOME - $POETRY_HOME/bin/pip install poetry==1.7.1 + $POETRY_HOME/bin/pip install poetry==1.8.4 $POETRY_HOME/bin/poetry --version - name: add poetry to path run: echo "${POETRY_HOME}/bin" >> $GITHUB_PATH diff --git a/README.md b/README.md index 90e1150..ef1639b 100644 --- a/README.md +++ b/README.md @@ -43,7 +43,7 @@ need the `neo4j_arrow` directory. # Build -This project uses [poetry]() as the build tool. +This project uses [poetry](https://python-poetry.org/) as the build tool. Install `poetry`, define your environment with `poetry env use` and invoke `poetry install` to install dependencies. To build; From b672e789a995c45348de61bf7309165dc3f334fc Mon Sep 17 00:00:00 2001 From: Ali Ince Date: Mon, 21 Oct 2024 17:56:47 +0100 Subject: [PATCH 6/8] Diagnose what is wrong in CI --- poetry.lock | 126 +++++++++++++++++++++++++++++++++- pyproject.toml | 1 + tests/integration/conftest.py | 10 +++ tox.ini | 3 +- 4 files changed, 137 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3892ead..67759de 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 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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--git a/tests/integration/conftest.py b/tests/integration/conftest.py index cabbb28..2a90716 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -2,6 +2,7 @@ from typing import Callable import neo4j +import pandas import pytest import testcontainers.neo4j @@ -10,6 +11,10 @@ def gds_version(driver: neo4j.Driver) -> str: + with driver.session() as session: + data = session.run("CALL gds.debug.sysInfo()").to_df() + print(data) + with driver.session() as session: version = session.run( "CALL gds.debug.sysInfo() YIELD key, value WITH * WHERE key = $key RETURN value", {"key": "gdsVersion"} @@ -55,6 +60,8 @@ def driver(neo4j): @pytest.fixture(scope="module") def arrow_client_factory(neo4j, driver) -> Callable[[str], Neo4jArrowClient]: def _arrow_client_factory(graph_name: str) -> Neo4jArrowClient: + print("neo4j inner username: " + neo4j.NEO4J_USER + "\n") + print("neo4j inner password: " + neo4j.NEO4J_ADMIN_PASSWORD + "\n") return Neo4jArrowClient( neo4j.get_container_host_ip(), graph=graph_name, @@ -65,6 +72,9 @@ def _arrow_client_factory(graph_name: str) -> Neo4jArrowClient: proc_names=neo4j_arrow._client.procedure_names(gds_version(driver)), ) + print("neo4j outer username: " + neo4j.NEO4J_USER + "\n") + print("neo4j outer password: " + neo4j.NEO4J_ADMIN_PASSWORD + "\n") + return _arrow_client_factory diff --git a/tox.ini b/tox.ini index c398b3d..6c33b96 100644 --- a/tox.ini +++ b/tox.ini @@ -6,6 +6,7 @@ deps = pytest neo4j testcontainers + pandas pyarrow10: pyarrow >= 10.0, < 11.0 pyarrow11: pyarrow >= 11.0, < 12.0 pyarrow12: pyarrow >= 12.0, < 13.0 @@ -18,7 +19,7 @@ warn_args = py{39,310,311,312}: -W error commands = unit: python -m pytest {[testenv]warn_args} -v {posargs} tests/unit - integration: python -m pytest -v {posargs} tests/integration + integration: python -m pytest -rP -v {posargs} tests/integration [testenv:py{39,310,311}-pyarrow{10,11,12,13,14,15,16,17}-unit] labels = unit From dfd3828e424b8efdc4ecc9b49ba7211c3fe033fd Mon Sep 17 00:00:00 2001 From: Ali Ince Date: Mon, 21 Oct 2024 18:07:43 +0100 Subject: [PATCH 7/8] Remove extra logging --- tests/integration/conftest.py | 6 ------ tox.ini | 2 +- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py index 2a90716..2fb1b7b 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -2,7 +2,6 @@ from typing import Callable import neo4j -import pandas import pytest import testcontainers.neo4j @@ -60,8 +59,6 @@ def driver(neo4j): @pytest.fixture(scope="module") def arrow_client_factory(neo4j, driver) -> Callable[[str], Neo4jArrowClient]: def _arrow_client_factory(graph_name: str) -> Neo4jArrowClient: - print("neo4j inner username: " + neo4j.NEO4J_USER + "\n") - print("neo4j inner password: " + neo4j.NEO4J_ADMIN_PASSWORD + "\n") return Neo4jArrowClient( neo4j.get_container_host_ip(), graph=graph_name, @@ -72,9 +69,6 @@ def _arrow_client_factory(graph_name: str) -> Neo4jArrowClient: proc_names=neo4j_arrow._client.procedure_names(gds_version(driver)), ) - print("neo4j outer username: " + neo4j.NEO4J_USER + "\n") - print("neo4j outer password: " + neo4j.NEO4J_ADMIN_PASSWORD + "\n") - return _arrow_client_factory diff --git a/tox.ini b/tox.ini index 6c33b96..3a31b38 100644 --- a/tox.ini +++ b/tox.ini @@ -19,7 +19,7 @@ warn_args = py{39,310,311,312}: -W error commands = unit: python -m pytest {[testenv]warn_args} -v {posargs} tests/unit - integration: python -m pytest -rP -v {posargs} tests/integration + integration: python -m pytest -rx -v {posargs} tests/integration [testenv:py{39,310,311}-pyarrow{10,11,12,13,14,15,16,17}-unit] labels = unit From 2340296690580ca377b57f2172ba593942ad66c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Max=20Kie=C3=9Fling?= Date: Wed, 23 Oct 2024 16:02:50 +0200 Subject: [PATCH 8/8] Read the ack message for each batch --- src/neo4j_arrow/_client.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/neo4j_arrow/_client.py b/src/neo4j_arrow/_client.py index a6a9371..edc35da 100644 --- a/src/neo4j_arrow/_client.py +++ b/src/neo4j_arrow/_client.py @@ -296,9 +296,9 @@ def _write_batches( for batch in batches: mapped_batch = fn(batch) self._write_batch_with_retries(mapped_batch, writer) + metadata_reader.read() # read the ack message n_rows += batch.num_rows n_bytes += batch.get_total_buffer_size() - metadata_reader.read() except Exception as e: raise error.interpret(e) return n_rows, n_bytes