From dcbfbb6c0fa075f118ae1e6d6a16ce5ae745ad3f Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Fri, 6 Dec 2024 12:46:16 -0800 Subject: [PATCH 1/2] Feature/update error logging (#138) * update python libraries * fix pylint * poetry update * update changelog * poetry update * add tests for concise exception class * more test coverage * update license --- .pylintrc | 3 +- CHANGELOG.md | 3 + LICENSE | 2 +- podaac/merger/harmony/cli.py | 2 +- podaac/merger/harmony/download_worker.py | 4 +- podaac/merger/harmony/service.py | 149 +- poetry.lock | 2599 ++++++++++++---------- pyproject.toml | 14 +- tests/test_concise_exception.py | 97 + 9 files changed, 1629 insertions(+), 1244 deletions(-) create mode 100644 tests/test_concise_exception.py diff --git a/.pylintrc b/.pylintrc index cd720bde..45714749 100644 --- a/.pylintrc +++ b/.pylintrc @@ -416,7 +416,8 @@ disable=raw-checker-failed, useless-suppression, deprecated-pragma, use-symbolic-message-instead, - too-many-arguments + too-many-arguments, + too-many-positional-arguments # Enable the message, report, category or checker with the given id(s). You can # either give multiple identifier separated by comma (,) or put this option diff --git a/CHANGELOG.md b/CHANGELOG.md index a592b317..c0646db9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added harmony deployment into github actions. ### Changed - [issue #117](https://github.com/podaac/concise/issues/117): Add part of URL to output file name + - Update python libraries + - Update harmony service lib that changed project structure + - Add Concise exception to propogate up to harmony api calls ### Deprecated ### Removed ### Fixed diff --git a/LICENSE b/LICENSE index f49a4e16..adb76827 100644 --- a/LICENSE +++ b/LICENSE @@ -186,7 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [yyyy] [name of copyright owner] + Copyright 2024 California Institute of Technology Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/podaac/merger/harmony/cli.py b/podaac/merger/harmony/cli.py index 3f0399bf..ece999ad 100644 --- a/podaac/merger/harmony/cli.py +++ b/podaac/merger/harmony/cli.py @@ -1,7 +1,7 @@ """A Harmony CLI wrapper around Concise""" from argparse import ArgumentParser -import harmony +import harmony_service_lib as harmony from podaac.merger.harmony.service import ConciseService diff --git a/podaac/merger/harmony/download_worker.py b/podaac/merger/harmony/download_worker.py index f4f3e2c9..51c8d03c 100644 --- a/podaac/merger/harmony/download_worker.py +++ b/podaac/merger/harmony/download_worker.py @@ -8,8 +8,8 @@ import re from urllib.parse import urlparse -from harmony.logging import build_logger -from harmony.util import download +from harmony_service_lib.logging import build_logger +from harmony_service_lib.util import download def multi_core_download(urls, destination_dir, access_token, cfg, process_count=None): diff --git a/podaac/merger/harmony/service.py b/podaac/merger/harmony/service.py index e2d5be51..a38deae0 100644 --- a/podaac/merger/harmony/service.py +++ b/podaac/merger/harmony/service.py @@ -6,9 +6,12 @@ from shutil import copyfile from urllib.parse import urlsplit from uuid import uuid4 +import traceback +import sys -from harmony.adapter import BaseHarmonyAdapter -from harmony.util import bbox_to_geometry, stage +from harmony_service_lib.adapter import BaseHarmonyAdapter +from harmony_service_lib.util import bbox_to_geometry, stage +from harmony_service_lib.exceptions import HarmonyException from pystac import Catalog, Item from pystac.item import Asset @@ -20,6 +23,37 @@ NETCDF4_MIME = 'application/x-netcdf4' # pylint: disable=invalid-name +class ConciseException(HarmonyException): + """Concise Exception class for custom error messages to see in harmony api calls.""" + def __init__(self, original_exception): + # Ensure we can extract traceback information + if original_exception.__traceback__ is None: + # Capture the current traceback if not already present + try: + raise original_exception + except type(original_exception): + original_exception.__traceback__ = sys.exc_info()[2] + + # Extract the last traceback entry (most recent call) for the error location + tb = traceback.extract_tb(original_exception.__traceback__)[-1] + + # Get the error details: file, line, function, and message + filename = tb.filename + lineno = tb.lineno + funcname = tb.name + error_msg = str(original_exception) + + # Format the error message to be more readable + readable_message = (f"Error in file '{filename}', line {lineno}, in function '{funcname}': " + f"{error_msg}") + + # Call the parent class constructor with the formatted message and category + super().__init__(readable_message, 'podaac/concise') + + # Store the original exception for potential further investigation + self.original_exception = original_exception + + class ConciseService(BaseHarmonyAdapter): """ A harmony-service-lib wrapper around the Concise module. This wrapper does @@ -55,63 +89,68 @@ def process_catalog(self, catalog: Catalog): pystac.Catalog A new catalog containing the results from the merge """ - result = catalog.clone() - result.id = str(uuid4()) - result.clear_children() - # Get all the items from the catalog, including from child or linked catalogs - items = list(self.get_all_catalog_items(catalog)) + try: + result = catalog.clone() + result.id = str(uuid4()) + result.clear_children() + + # Get all the items from the catalog, including from child or linked catalogs + items = list(self.get_all_catalog_items(catalog)) + + # Quick return if catalog contains no items + if len(items) == 0: + return result + + # -- Process metadata -- + bbox = [] + granule_urls = [] + datetimes = [ + datetime.max.replace(tzinfo=timezone.utc), # start + datetime.min.replace(tzinfo=timezone.utc) # end + ] + + for item in items: + get_bbox(item, bbox) + get_granule_url(item, granule_urls) + get_datetime(item, datetimes) + + # Items did not have a bbox; valid under spec + if len(bbox) == 0: + bbox = None + + # -- Perform merging -- + collection = self._get_item_source(items[0]).collection + first_granule_url = [] + get_granule_url(items[0], first_granule_url) + first_url_name = Path(first_granule_url[0]).stem + filename = f'{first_url_name}_{datetimes[1].strftime("%Y%m%dT%H%M%SZ")}_{collection}_merged.nc4' + + with TemporaryDirectory() as temp_dir: + self.logger.info('Starting granule downloads') + input_files = multi_core_download(granule_urls, temp_dir, self.message.accessToken, self.config) + self.logger.info('Finished granule downloads') + + output_path = Path(temp_dir).joinpath(filename).resolve() + merge_netcdf_files(input_files, output_path, granule_urls, logger=self.logger) + staged_url = self._stage(str(output_path), filename, NETCDF4_MIME) + + # -- Output to STAC catalog -- + result.clear_items() + properties = { + "start_datetime": datetimes[0].isoformat(), + "end_datetime": datetimes[1].isoformat() + } + + item = Item(str(uuid4()), bbox_to_geometry(bbox), bbox, None, properties) + asset = Asset(staged_url, title=filename, media_type=NETCDF4_MIME, roles=['data']) + item.add_asset('data', asset) + result.add_item(item) - # Quick return if catalog contains no items - if len(items) == 0: return result - # -- Process metadata -- - bbox = [] - granule_urls = [] - datetimes = [ - datetime.max.replace(tzinfo=timezone.utc), # start - datetime.min.replace(tzinfo=timezone.utc) # end - ] - - for item in items: - get_bbox(item, bbox) - get_granule_url(item, granule_urls) - get_datetime(item, datetimes) - - # Items did not have a bbox; valid under spec - if len(bbox) == 0: - bbox = None - - # -- Perform merging -- - collection = self._get_item_source(items[0]).collection - first_granule_url = [] - get_granule_url(items[0], first_granule_url) - first_url_name = Path(first_granule_url[0]).stem - filename = f'{first_url_name}_{datetimes[1].strftime("%Y%m%dT%H%M%SZ")}_{collection}_merged.nc4' - - with TemporaryDirectory() as temp_dir: - self.logger.info('Starting granule downloads') - input_files = multi_core_download(granule_urls, temp_dir, self.message.accessToken, self.config) - self.logger.info('Finished granule downloads') - - output_path = Path(temp_dir).joinpath(filename).resolve() - merge_netcdf_files(input_files, output_path, granule_urls, logger=self.logger) - staged_url = self._stage(str(output_path), filename, NETCDF4_MIME) - - # -- Output to STAC catalog -- - result.clear_items() - properties = { - "start_datetime": datetimes[0].isoformat(), - "end_datetime": datetimes[1].isoformat() - } - - item = Item(str(uuid4()), bbox_to_geometry(bbox), bbox, None, properties) - asset = Asset(staged_url, title=filename, media_type=NETCDF4_MIME, roles=['data']) - item.add_asset('data', asset) - result.add_item(item) - - return result + except Exception as ex: + raise ConciseException(ex) from ex def _stage(self, local_filename, remote_filename, mime): """ diff --git a/poetry.lock b/poetry.lock index 72c30584..d3cd69e1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,109 +1,109 @@ -# 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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+import traceback +import sys +from podaac.merger.harmony.service import ConciseException + + +def test_exception_message_formatting(): + """ + Test that the ConciseException correctly formats the error message + with file, line, function, and original error details. + """ + try: + # Simulate an error by intentionally causing a division by zero + 1 / 0 + except ZeroDivisionError as original_error: + concise_exception = ConciseException(original_error) + + # Detailed assertions with informative error messages + error_str = str(concise_exception) + error_msg = concise_exception.message + + assert "Error in file" in error_msg, f"Expected file context, got: {error_msg}" + assert "line" in error_msg, f"Expected line number, got: {error_msg}" + assert "in function" in error_msg, f"Expected function context, got: {error_msg}" + assert "division by zero" in error_msg, f"Expected original error message, got: {error_msg}" + assert concise_exception.category == 'podaac/concise' + +def test_exception_traceback_details(): + """ + Verify that the exception captures the correct traceback information. + """ + def inner_function(): + # Another function to add depth to the traceback + 1 / 0 + + try: + inner_function() + except ZeroDivisionError as original_error: + concise_exception = ConciseException(original_error) + + # Extract expected details + tb = traceback.extract_tb(original_error.__traceback__)[-1] + expected_filename = tb.filename + expected_lineno = tb.lineno + expected_funcname = tb.name + + error_msg = concise_exception.message + assert expected_filename in error_msg, f"Filename not found, got: {error_msg}" + assert str(expected_lineno) in error_msg, f"Line number not found, got: {error_msg}" + assert expected_funcname in error_msg, f"Function name not found, got: {error_msg}" + +def test_original_error_type_preservation(): + """ + Ensure that the original error type is preserved in the traceback. + """ + try: + raise ValueError("Test error message") + except ValueError as original_error: + concise_exception = ConciseException(original_error) + + error_msg = concise_exception.message + assert "Test error message" in error_msg, f"Original error message not found, got: {error_msg}" + assert isinstance(concise_exception.original_exception, ValueError) + +def test_module_identifier(): + """ + Verify that the module identifier is set correctly. + """ + try: + raise RuntimeError("Sample error") + except RuntimeError as original_error: + concise_exception = ConciseException(original_error) + + assert concise_exception.category == 'podaac/concise' + +def test_exception_with_no_traceback(): + """ + Test handling of an exception without an existing traceback. + """ + # Create an exception without a traceback + try: + raise ValueError("Test exception without traceback") + except ValueError as original_error: + # Deliberately remove the traceback + original_error.__traceback__ = None + + # Create ConciseException + concise_exception = ConciseException(original_error) + + # Verify that a traceback was generated + assert concise_exception.original_exception is not None + + # Check that the message is still formatted + error_msg = concise_exception.message + assert "Error in file" in error_msg + assert "in function" in error_msg + assert "Test exception without traceback" in error_msg From 9ecc008dace259669cbf3abb87486625a2dd6cbe Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 6 Dec 2024 20:49:04 +0000 Subject: [PATCH 2/2] /version 0.10.0a6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ab9994ca..0f00940b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a5" +version = "0.10.0a6" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0"