From d6de45d7832ef4864286f349ba872fb8277cfb33 Mon Sep 17 00:00:00 2001 From: Julius Unverfehrt Date: Thu, 16 Mar 2023 16:08:44 +0100 Subject: [PATCH] Pull request #65: RED-6205 monitoring Merge in RR/pyinfra from RED-6205-monitoring to master Squashed commit of the following: commit 529cedfd7c065a3f7364e4596b923f25f0af76b5 Author: Matthias Bisping Date: Thu Mar 16 14:57:26 2023 +0100 Remove unnecessary default argument to dict.get commit b718531f568e89df77cc05039e5e7afe7111b9a4 Author: Julius Unverfehrt Date: Thu Mar 16 14:56:50 2023 +0100 refactor commit c039b0c25a6cd2ad2a72d237d0930c484c8e427c Author: Julius Unverfehrt Date: Thu Mar 16 13:22:17 2023 +0100 increase package version to reflect the recent changes commit 0a983a4113f25cd692b68869e1f33ffbf7efc6f0 Author: Julius Unverfehrt Date: Thu Mar 16 13:16:39 2023 +0100 remove processing result conversion to a list, since ner-predicion service actually returns a dictionary. It is now expected that the result is sized to perform the monitoring and json dumpable to upload it. commit 541bf321410471dc09a354669b2778402286c09f Author: Julius Unverfehrt Date: Thu Mar 16 12:48:07 2023 +0100 remove no longer needed requirements commit cfa182985d989a5b92a9a069a603daee72f37d49 Author: Julius Unverfehrt Date: Thu Mar 16 11:14:58 2023 +0100 refactor payload formatting - introduce PayloadFormatter class for better typehinting and bundling of functionality - parametrize payload formatting so the PayloadProcesser can adapt better to differnt services/products - move file extension parsing to its own module commit f57663b86954b7164eeb6db013d862af88ec4584 Author: Julius Unverfehrt Date: Wed Mar 15 12:22:08 2023 +0100 refactor payload parsing - introduce QueueMessagePayloadParser for generality and typehinting - refactor file extension parsing algorithm commit 713fb4a0dddecf5442ceda3988444d9887869dcf Author: Julius Unverfehrt Date: Tue Mar 14 17:07:02 2023 +0100 fix tests commit a22ecf7ae93bc0bec235fba3fd9cbf6c1778aa13 Author: Julius Unverfehrt Date: Tue Mar 14 16:31:26 2023 +0100 refactor payload parsing - parameterize file and compression types allowed for files to download and upload via config - make a real value bag out of QueueMessagePayload and do the parsing beforehand - refector file extension parser to be more robust commit 50b578d054ca47a94c907f5f8b585eca7ed626ac Author: Julius Unverfehrt Date: Tue Mar 14 13:21:32 2023 +0100 add monitoring - add an optional prometheus monitor to monitor the average processing time of a service per relevent paramater that is at this point defined via the number of resulting elements. commit de525e7fa2f846f7fde5b9a4b466039238da10cd Author: Julius Unverfehrt Date: Tue Mar 14 12:57:24 2023 +0100 fix bug in file extension parser not working if the file endings have prefixes --- README.md | 4 + poetry.lock | 748 +++++++++++------------- pyinfra/config.py | 21 + pyinfra/payload_processing/monitor.py | 62 ++ pyinfra/payload_processing/payload.py | 102 ++-- pyinfra/payload_processing/processor.py | 41 +- pyinfra/utils/file_extension_parsing.py | 41 ++ pyproject.toml | 3 +- tests/monitor_test.py | 46 ++ tests/payload_test.py | 44 ++ tests/processing_test.py | 7 + 11 files changed, 676 insertions(+), 443 deletions(-) create mode 100644 pyinfra/payload_processing/monitor.py create mode 100644 pyinfra/utils/file_extension_parsing.py create mode 100644 tests/monitor_test.py create mode 100644 tests/payload_test.py diff --git a/README.md b/README.md index c1b0181..f274497 100755 --- a/README.md +++ b/README.md @@ -19,6 +19,10 @@ A configuration is located in `/config.yaml`. All relevant variables can be conf | Environment Variable | Default | Description | |-------------------------------|----------------------------------|--------------------------------------------------------------------------| | LOGGING_LEVEL_ROOT | "DEBUG" | Logging level for service logger | +| MONITORING_ENABLED | True | Enables Prometheus monitoring | +| PROMETHEUS_METRIC_PREFIX | "redactmanager_research_service" | Prometheus metric prefix, per convention '{product_name}_{service name}' | +| PROMETHEUS_HOST | "127.0.0.1" | Prometheus webserver address | +| PROMETHEUS_PORT | 8080 | Prometheus webserver port | | RABBITMQ_HOST | "localhost" | RabbitMQ host address | | RABBITMQ_PORT | "5672" | RabbitMQ host port | | RABBITMQ_USERNAME | "user" | RabbitMQ username | diff --git a/poetry.lock b/poetry.lock index 6d86796..9e6c96e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,14 +14,14 @@ files = [ [[package]] name = "astroid" -version = "2.14.2" +version = "2.15.0" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false python-versions = ">=3.7.2" files = [ - {file = "astroid-2.14.2-py3-none-any.whl", hash = "sha256:0e0e3709d64fbffd3037e4ff403580550f14471fd3eaae9fa11cc9a5c7901153"}, - {file = "astroid-2.14.2.tar.gz", hash = "sha256:a3cf9f02c53dd259144a7e8f3ccd75d67c9a8c716ef183e0c1f291bc5d7bb3cf"}, + {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"}, + {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"}, ] [package.dependencies] @@ -287,100 +287,87 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.0.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. 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normalize_bool(read_from_environment("MONITORING_ENABLED", True)) + + # Prometheus metric prefix, per convention '{product_name}_{service_name}_{parameter}' + # In the current implementation, the results of a service define the parameter that is monitored, + # i.e. analysis result per image means processing time per image is monitored. + # TODO: add validator since some characters like '-' are not allowed by python prometheus + self.prometheus_metric_prefix = read_from_environment( + "PROMETHEUS_METRIC_PREFIX", "redactmanager_research_service_parameter" + ) + + # Prometheus webserver address + self.prometheus_host = read_from_environment("PROMETHEUS_HOST", "127.0.0.1") + + # Prometheus webserver port + self.prometheus_port = int(read_from_environment("PROMETHEUS_PORT", 8080)) + # RabbitMQ host address self.rabbitmq_host = read_from_environment("RABBITMQ_HOST", "localhost") @@ -73,6 +90,10 @@ class Config: "DefaultEndpointsProtocol=...", ) + # Allowed file types for downloaded and uploaded storage objects that get processed by the service + self.allowed_file_types = ["json", "pdf"] + self.allowed_compression_types = ["gz"] + # Value to see if we should write a consumer token to a file self.write_consumer_token = read_from_environment("WRITE_CONSUMER_TOKEN", "False") diff --git a/pyinfra/payload_processing/monitor.py b/pyinfra/payload_processing/monitor.py new file mode 100644 index 0000000..ebcd714 --- /dev/null +++ b/pyinfra/payload_processing/monitor.py @@ -0,0 +1,62 @@ +import logging +from operator import attrgetter +from time import time +from typing import Callable, Any, Sized + +from funcy import identity +from prometheus_client import Summary, start_http_server, CollectorRegistry + +from pyinfra.config import Config + +logger = logging.getLogger() + + +class PrometheusMonitor: + def __init__(self, prefix: str, port=8080, host="127.0.0.1"): + """Register the monitoring metrics and start a webserver where they can be scraped at the endpoint + http://{host}:{port}/prometheus + + Args: + prefix: should per convention consist of {product_name}_{service_name}_{parameter_to_monitor} + parameter_to_monitor is defined by the result of the processing service. + """ + self.registry = CollectorRegistry() + + self.entity_processing_time_sum = Summary( + f"{prefix}_processing_time", + "Summed up average processing time per entity observed", + ) + + self.registry.register(self.entity_processing_time_sum) + + start_http_server(port, host, self.registry) + + def __call__(self, process_fn: Callable) -> Callable: + """Monitor the runtime of a function and update the registered metric with the average runtime per resulting + element. + """ + return self._add_result_monitoring(process_fn) + + def _add_result_monitoring(self, process_fn: Callable): + def inner(data: Any): + + start = time() + + result: Sized = process_fn(data) + + runtime = time() - start + + processing_time_per_entity = runtime / len(result) + + self.entity_processing_time_sum.observe(processing_time_per_entity) + + return result + + return inner + + +def get_monitor(config: Config) -> Callable: + if config.monitoring_enabled: + return PrometheusMonitor(*attrgetter("prometheus_metric_prefix", "prometheus_port", "prometheus_host")(config)) + else: + return identity diff --git a/pyinfra/payload_processing/payload.py b/pyinfra/payload_processing/payload.py index 79c63c2..48d4bd2 100644 --- a/pyinfra/payload_processing/payload.py +++ b/pyinfra/payload_processing/payload.py @@ -1,7 +1,10 @@ -import os -from dataclasses import dataclass, field +from dataclasses import dataclass +from itertools import chain from operator import itemgetter -from typing import List, Tuple +from typing import Union, Sized + +from pyinfra.config import Config +from pyinfra.utils.file_extension_parsing import make_file_extension_parser @dataclass @@ -11,46 +14,73 @@ class QueueMessagePayload: target_file_extension: str response_file_extension: str - target_file_name: str = field(init=False) - response_file_name: str = field(init=False) + target_file_type: Union[str, None] + target_compression_type: Union[str, None] + response_file_type: Union[str, None] + response_compression_type: Union[str, None] - def __post_init__(self): - self.target_file_name = f"{self.dossier_id}/{self.file_id}.{self.target_file_extension}" - self.response_file_name = f"{self.dossier_id}/{self.file_id}.{self.response_file_extension}" - - self.target_file_type, self.target_compression_type = parse_file_extension(self.target_file_extension) - self.response_file_type, self.response_compression_type = parse_file_extension(self.response_file_extension) + target_file_name: str + response_file_name: str -def read_queue_message_payload(payload: dict) -> QueueMessagePayload: - return QueueMessagePayload( - *itemgetter( - "dossierId", - "fileId", - "targetFileExtension", - "responseFileExtension", +class QueueMessagePayloadParser: + def __init__(self, file_extension_parser): + self.parse_file_extensions = file_extension_parser + + def __call__(self, payload: dict) -> QueueMessagePayload: + """Translate the queue message payload to the internal QueueMessagePayload object.""" + return self._parse_queue_message_payload(payload) + + def _parse_queue_message_payload(self, payload: dict) -> QueueMessagePayload: + dossier_id, file_id, target_file_extension, response_file_extension = itemgetter( + "dossierId", "fileId", "targetFileExtension", "responseFileExtension" )(payload) - ) + + target_file_type, target_compression_type, response_file_type, response_compression_type = chain.from_iterable( + map(self.parse_file_extensions, [target_file_extension, response_file_extension]) + ) + + target_file_name = f"{dossier_id}/{file_id}.{target_file_extension}" + response_file_name = f"{dossier_id}/{file_id}.{response_file_extension}" + + return QueueMessagePayload( + dossier_id=dossier_id, + file_id=file_id, + target_file_extension=target_file_extension, + response_file_extension=response_file_extension, + target_file_type=target_file_type, + target_compression_type=target_compression_type, + response_file_type=response_file_type, + response_compression_type=response_compression_type, + target_file_name=target_file_name, + response_file_name=response_file_name, + ) -def format_service_processing_result_for_storage( - queue_message_payload: QueueMessagePayload, service_processing_result: List[dict] -) -> dict: - return { - "dossierId": queue_message_payload.dossier_id, - "fileId": queue_message_payload.file_id, - "targetFileExtension": queue_message_payload.target_file_extension, - "responseFileExtension": queue_message_payload.response_file_extension, - "data": service_processing_result, - } +def get_queue_message_payload_parser(config: Config) -> QueueMessagePayloadParser: + file_extension_parser = make_file_extension_parser(config.allowed_file_types, config.allowed_compression_types) + return QueueMessagePayloadParser(file_extension_parser) -def format_to_queue_message_response_body(queue_message_payload: QueueMessagePayload) -> dict: - return {"dossierId": queue_message_payload.dossier_id, "fileId": queue_message_payload.file_id} +class QueueMessagePayloadFormatter: + @staticmethod + def format_service_processing_result_for_storage( + queue_message_payload: QueueMessagePayload, service_processing_result: Sized + ) -> dict: + """Format the results of a processing function with the QueueMessagePayload for the storage upload.""" + return { + "dossierId": queue_message_payload.dossier_id, + "fileId": queue_message_payload.file_id, + "targetFileExtension": queue_message_payload.target_file_extension, + "responseFileExtension": queue_message_payload.response_file_extension, + "data": service_processing_result, + } + + @staticmethod + def format_to_queue_message_response_body(queue_message_payload: QueueMessagePayload) -> dict: + """Format QueueMessagePayload for the AMPQ response after processing.""" + return {"dossierId": queue_message_payload.dossier_id, "fileId": queue_message_payload.file_id} -def parse_file_extension(file_extension: str) -> Tuple[str, str]: - file_type, compression_type = os.path.splitext(file_extension) - if "." in file_type: - raise ValueError(f"Number of file extensions exceeds allowed amount of two: {file_extension}") - return file_type, compression_type +def get_queue_message_payload_formatter() -> QueueMessagePayloadFormatter: + return QueueMessagePayloadFormatter() diff --git a/pyinfra/payload_processing/processor.py b/pyinfra/payload_processing/processor.py index 08fd333..ebfcf81 100644 --- a/pyinfra/payload_processing/processor.py +++ b/pyinfra/payload_processing/processor.py @@ -6,10 +6,12 @@ from typing import Callable, Union, List from funcy import compose from pyinfra.config import get_config, Config +from pyinfra.payload_processing.monitor import get_monitor from pyinfra.payload_processing.payload import ( - read_queue_message_payload, - format_service_processing_result_for_storage, - format_to_queue_message_response_body, + QueueMessagePayloadParser, + get_queue_message_payload_parser, + QueueMessagePayloadFormatter, + get_queue_message_payload_formatter, ) from pyinfra.storage import get_storage from pyinfra.storage.storage import make_downloader, make_uploader @@ -20,14 +22,28 @@ logger.setLevel(get_config().logging_level_root) class PayloadProcessor: - def __init__(self, storage: Storage, bucket: str, data_processor: Callable): + def __init__( + self, + storage: Storage, + bucket: str, + payload_parser: QueueMessagePayloadParser, + payload_formatter: QueueMessagePayloadFormatter, + data_processor: Callable, + ): """Wraps an analysis function specified by a service (e.g. NER service) in pre- and post-processing steps. Args: storage: The storage to use for downloading and uploading files bucket: The bucket to use for downloading and uploading files + payload_parser: Parser that translates the queue message payload to the required QueueMessagePayload object + payload_formatter: Formatter for the storage upload result and the queue message response body data_processor: The analysis function to be called with the downloaded file + NOTE: the result of the analysis function has to be Sized, e.g. a dict or a list to be able to upload it + and to be able to monitor the processing time. """ + self.parse_payload = payload_parser + self.format_result_for_storage = payload_formatter.format_service_processing_result_for_storage + self.format_to_queue_message_response_body = payload_formatter.format_to_queue_message_response_body self.process_data = data_processor self.partial_download_fn = partial(make_downloader, storage, bucket) @@ -52,12 +68,12 @@ class PayloadProcessor: return self._process(queue_message_payload) def _process(self, queue_message_payload: dict) -> dict: - payload = read_queue_message_payload(queue_message_payload) + payload = self.parse_payload(queue_message_payload) logger.info(f"Processing {asdict(payload)} ...") download_file_to_process = self.partial_download_fn(payload.target_file_type, payload.target_compression_type) upload_processing_result = self.partial_upload_fn(payload.response_file_type, payload.response_compression_type) - format_result_for_storage = partial(format_service_processing_result_for_storage, payload) + format_result_for_storage = partial(self.format_result_for_storage, payload) processing_pipeline = compose(format_result_for_storage, self.process_data, download_file_to_process) @@ -65,16 +81,19 @@ class PayloadProcessor: upload_processing_result(payload.response_file_name, result) - return format_to_queue_message_response_body(payload) + return self.format_to_queue_message_response_body(payload) -def make_payload_processor(data_processor: Callable, config: Union[None, Config]) -> PayloadProcessor: +def make_payload_processor(data_processor: Callable, config: Union[None, Config] = None) -> PayloadProcessor: """Produces payload processor for queue manager.""" config = config or get_config() - storage: Storage = get_storage(config) bucket: str = config.storage_bucket + storage: Storage = get_storage(config) + monitor = get_monitor(config) + payload_parser: QueueMessagePayloadParser = get_queue_message_payload_parser(config) + payload_formatter: QueueMessagePayloadFormatter = get_queue_message_payload_formatter() - data_processor = compose(list, data_processor) + data_processor = monitor(data_processor) - return PayloadProcessor(storage, bucket, data_processor) + return PayloadProcessor(storage, bucket, payload_parser, payload_formatter, data_processor) diff --git a/pyinfra/utils/file_extension_parsing.py b/pyinfra/utils/file_extension_parsing.py new file mode 100644 index 0000000..2eb0d3f --- /dev/null +++ b/pyinfra/utils/file_extension_parsing.py @@ -0,0 +1,41 @@ +from collections import defaultdict +from typing import Callable + +from funcy import merge + + +def make_file_extension_parser(file_types, compression_types): + ext2_type2ext = make_ext2_type2ext(file_types, compression_types) + ext_to_type2ext = make_ext_to_type2ext(ext2_type2ext) + + def inner(path): + file_extensions = parse_file_extensions(path, ext_to_type2ext) + return file_extensions.get("file_type"), file_extensions.get("compression_type") + + return inner + + +def make_ext2_type2ext(file_type_extensions, compression_type_extensions): + def make_ext_to_ext2type(ext_type): + return lambda ext: {ext_type: ext} + + ext_to_file_type_mapper = make_ext_to_ext2type("file_type") + ext_to_compression_type_mapper = make_ext_to_ext2type("compression_type") + return defaultdict( + lambda: lambda _: {}, + { + **{e: ext_to_file_type_mapper for e in file_type_extensions}, + **{e: ext_to_compression_type_mapper for e in compression_type_extensions}, + }, + ) + + +def make_ext_to_type2ext(ext2_type2ext): + def ext_to_type2ext(ext): + return ext2_type2ext[ext](ext) + + return ext_to_type2ext + + +def parse_file_extensions(path, ext_to_type2ext: Callable): + return merge(*map(ext_to_type2ext, path.split("."))) diff --git a/pyproject.toml b/pyproject.toml index 4be65a7..3a513dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pyinfra" -version = "1.4.1" +version = "1.5.0" description = "" authors = ["Francisco Schulz "] license = "All rights reseverd" @@ -17,7 +17,6 @@ testcontainers = "3.4.2" docker-compose = "1.29.2" funcy = "1.17" prometheus-client = "^0.16.0" -pymupdf = "^1.21.1" [tool.poetry.group.dev.dependencies] pytest = "^7.1.3" diff --git a/tests/monitor_test.py b/tests/monitor_test.py new file mode 100644 index 0000000..391e681 --- /dev/null +++ b/tests/monitor_test.py @@ -0,0 +1,46 @@ +import re +import time + +import pytest +import requests + +from pyinfra.config import get_config +from pyinfra.payload_processing.monitor import get_monitor + + +@pytest.fixture(scope="class") +def monitor_config(): + config = get_config() + config.prometheus_metric_prefix = "monitor_test" + config.prometheus_port = 8000 + return config + + +@pytest.fixture(scope="class") +def prometheus_monitor(monitor_config): + return get_monitor(monitor_config) + + +@pytest.fixture +def monitored_mock_function(prometheus_monitor): + def process(data=None): + time.sleep(2) + return ["result1", "result2", "result3"] + + return prometheus_monitor(process) + + +class TestPrometheusMonitor: + def test_prometheus_endpoint_is_available(self, prometheus_monitor, monitor_config): + resp = requests.get(f"http://{monitor_config.prometheus_host}:{monitor_config.prometheus_port}/prometheus") + assert resp.status_code == 200 + + def test_processing_with_a_monitored_fn_increases_parameter_counter(self, monitored_mock_function, monitor_config): + monitored_mock_function(data=None) + resp = requests.get(f"http://{monitor_config.prometheus_host}:{monitor_config.prometheus_port}/prometheus") + pattern = re.compile(r".*monitor_test_processing_time_count (\d\.\d).*") + assert pattern.search(resp.text).group(1) == "1.0" + + monitored_mock_function(data=None) + resp = requests.get(f"http://{monitor_config.prometheus_host}:{monitor_config.prometheus_port}/prometheus") + assert pattern.search(resp.text).group(1) == "2.0" diff --git a/tests/payload_test.py b/tests/payload_test.py new file mode 100644 index 0000000..5f0bb36 --- /dev/null +++ b/tests/payload_test.py @@ -0,0 +1,44 @@ +import pytest + +from pyinfra.config import get_config +from pyinfra.payload_processing.payload import ( + QueueMessagePayload, + get_queue_message_payload_parser, +) +from pyinfra.utils.file_extension_parsing import make_file_extension_parser + + +@pytest.fixture(scope="session") +def payload_config(): + return get_config() + + +class TestPayload: + def test_payload_is_parsed_correctly(self, request_payload, payload_config): + parse_payload = get_queue_message_payload_parser(payload_config) + payload = parse_payload(request_payload) + assert payload == QueueMessagePayload( + dossier_id="test", + file_id="test", + target_file_extension="json.gz", + response_file_extension="json.gz", + target_file_type="json", + target_compression_type="gz", + response_file_type="json", + response_compression_type="gz", + target_file_name="test/test.json.gz", + response_file_name="test/test.json.gz", + ) + + @pytest.mark.parametrize( + "extension,expected", + [ + ("json.gz", ("json", "gz")), + ("json", ("json", None)), + ("prefix.json.gz", ("json", "gz")), + ], + ) + @pytest.mark.parametrize("allowed_file_types,allowed_compression_types", [(["json", "pdf"], ["gz"])]) + def test_parse_file_extension(self, extension, expected, allowed_file_types, allowed_compression_types): + parse = make_file_extension_parser(allowed_file_types, allowed_compression_types) + assert parse(extension) == expected diff --git a/tests/processing_test.py b/tests/processing_test.py index ec83a40..18698d7 100644 --- a/tests/processing_test.py +++ b/tests/processing_test.py @@ -3,6 +3,7 @@ import json from operator import itemgetter import pytest +import requests from pyinfra.payload_processing.processor import make_payload_processor @@ -67,3 +68,9 @@ class TestPayloadProcessor: storage.clear_bucket(bucket_name) with pytest.raises(Exception): payload_processor(request_payload) + + def test_prometheus_endpoint_is_available(self, processing_config): + resp = requests.get( + f"http://{processing_config.prometheus_host}:{processing_config.prometheus_port}/prometheus" + ) + assert resp.status_code == 200 \ No newline at end of file