diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index c28f1a0e..3bed15f8 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -85,7 +85,7 @@ jobs: run: | poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=xml:build/reports/coverage.xml -m "not aws and not integration" tests/ - name: SonarCloud Scan - uses: sonarsource/sonarcloud-github-action@master + uses: sonarsource/sonarqube-scan-action@v4 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} @@ -243,6 +243,29 @@ jobs: pull: true tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} + - name: Deploy Harmony + env: + ENV: ${{ env.venue }} + CMR_USER: ${{ secrets.CMR_USER }} + CMR_PASS: ${{ secrets.CMR_PASS }} + if: | + github.ref == 'refs/heads/main' || + startsWith(github.ref, 'refs/heads/release') + working-directory: deployment + run: + poetry run python harmony_deploy.py --tag ${{ env.software_version }} + - name: Create Release + id: create_release + if: | + github.ref == 'refs/heads/main' + uses: softprops/action-gh-release@v2 + with: + tag_name: "${{ env.software_version }}" # Use the tag that triggered the action + release_name: Release v{{ env.software_version }} + draft: false + generate_release_notes: true + token: ${{ secrets.GITHUB_TOKEN }} + # As of 2023/01/23 these steps below for scanning the Docker image with Snyk are failing. I've tried both the official Snyk # action https://github.com/snyk/actions/tree/master/docker and this method below of manually calling the CLI. # The error when using the official Snyk action is 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 6a3694a6..acb92c03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +## [0.10.0] + +### Added + - Update Github Actions + - 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 + - Variable Merging + - Fixed way we merge variables when granules in a collection have varying variables. + + ## [0.9.0] ### Added 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/deployment/harmony_deploy.py b/deployment/harmony_deploy.py new file mode 100644 index 00000000..df0c913f --- /dev/null +++ b/deployment/harmony_deploy.py @@ -0,0 +1,64 @@ +import os +import requests +import json +import logging +import argparse +from requests.auth import HTTPBasicAuth + +# Environment variables +ENV = os.getenv('ENV') +CMR_USER = os.getenv('CMR_USER') +CMR_PASS = os.getenv('CMR_PASS') + +def bearer_token() -> str: + tokens = [] + headers = {'Accept': 'application/json'} + url = f"https://{'uat.' if ENV == 'uat' else ''}urs.earthdata.nasa.gov/api/users" + + # First just try to get a token that already exists + try: + resp = requests.get(url + "/tokens", headers=headers, auth=HTTPBasicAuth(CMR_USER, CMR_PASS)) + response_content = json.loads(resp.content) + + for x in response_content: + tokens.append(x['access_token']) + + except Exception: # noqa E722 + logging.warning("Error getting the token - check user name and password", exc_info=True) + + # No tokens exist, try to create one + if not tokens: + try: + resp = requests.post(url + "/token", headers=headers, auth=HTTPBasicAuth(CMR_USER, CMR_PASS)) + response_content = json.loads(resp.content) + tokens.append(response_content['access_token']) + except Exception: # noqa E722 + logging.warning("Error getting the token - check user name and password", exc_info=True) + + # If still no token, then we can't do anything + if not tokens: + raise RuntimeError("Unable to get bearer token from EDL") + + return next(iter(tokens)) + +if __name__ == "__main__": + + parser = argparse.ArgumentParser(description="Update the service image tag.") + parser.add_argument("--tag", help="The new tag version to update.", required=True) + args = parser.parse_args() + + url = f"https://harmony.{'uat.' if ENV == 'uat' else ''}earthdata.nasa.gov/service-image-tag/podaac-concise" + token = bearer_token() + + headers = { + "Authorization": f"Bearer {token}", + "Content-type": "application/json" + } + data = { + "tag": args.tag + } + + response = requests.put(url, headers=headers, json=data) + response.raise_for_status() + + print(f"Response JSON: {response.json()}") 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 d8013196..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 @@ -32,7 +66,7 @@ def invoke(self): Primary entrypoint into the service wrapper. Overrides BaseHarmonyAdapter.invoke """ if not self.catalog: - # Message-only support is being depreciated in Harmony so we should expect to + # Message-only support is being depreciated in Harmony, so we should expect to # only see requests with catalogs when invoked with a newer Harmony instance # https://github.com/nasa/harmony-service-lib-py/blob/21bcfbda17caf626fb14d2ac4f8673be9726b549/harmony/adapter.py#L71 raise RuntimeError('Invoking CONCISE without a STAC catalog is not supported') @@ -42,7 +76,7 @@ def invoke(self): def process_catalog(self, catalog: Catalog): """ Recursively process a catalog and all its children. Adapted from - BaseHarmonyAdapter._process_catalog_recursive to specfifically + BaseHarmonyAdapter._process_catalog_recursive to specifically support our particular use case for many-to-one Parameters @@ -55,60 +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 - filename = f'{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/podaac/merger/merge.py b/podaac/merger/merge.py index 44a20503..a9d10be3 100644 --- a/podaac/merger/merge.py +++ b/podaac/merger/merge.py @@ -24,7 +24,7 @@ def is_file_empty(parent_group: nc.Dataset | nc.Group) -> bool: return True -def merge_netcdf_files(original_input_files: list[Path], # pylint: disable=too-many-locals +def merge_netcdf_files(original_input_files: list[Path], # pylint: disable=too-many-locals,too-many-positional-arguments output_file: str, granule_urls, logger=getLogger(__name__), diff --git a/podaac/merger/merge_worker.py b/podaac/merger/merge_worker.py index d43ee66a..3c3880c2 100644 --- a/podaac/merger/merge_worker.py +++ b/podaac/merger/merge_worker.py @@ -58,6 +58,7 @@ def max_var_memory(file_list: list[Path], var_info: dict, max_dims) -> int: return max_var_mem +# pylint: disable=too-many-positional-arguments def run_merge(merged_dataset: nc.Dataset, file_list: list[Path], var_info: dict, diff --git a/podaac/merger/preprocess_worker.py b/podaac/merger/preprocess_worker.py index 4bedba33..82446d3a 100644 --- a/podaac/merger/preprocess_worker.py +++ b/podaac/merger/preprocess_worker.py @@ -236,14 +236,10 @@ def _run_multi_core(file_list: list[Path], if var_info is None: var_info = result['var_info'] elif var_info != result['var_info']: - if set(var_info.keys()).difference(result['var_info']): - # If not all variables match, only compare variables that intersect - intersecting_vars = set(var_info).intersection(result['var_info']) - if list( - map(var_info.get, intersecting_vars) - ) != list(map(result['var_info'].get, intersecting_vars)): - raise RuntimeError('Variable schemas are inconsistent between granules') - var_info.update(result['var_info']) + intersecting_vars = set(var_info).intersection(result['var_info']) + if any(var_info[var] != result['var_info'][var] for var in intersecting_vars): + raise RuntimeError('Variable schemas are inconsistent between granules') + var_info.update(result['var_info']) # The 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+version = "0.10.0rc11" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" @@ -17,19 +17,19 @@ packages = [ [tool.poetry.dependencies] python = "^3.10" netCDF4 = "^1.5.6" -numpy = "^1.20.3" -harmony-service-lib = "^1.0.27" -importlib-metadata = "^7.1.0" +numpy = "^2.1.3" +harmony-service-lib = "^2.4.0" +importlib-metadata = "^8.5.0" [tool.poetry.group.dev.dependencies] -setuptools = "^70.0.0" +setuptools = "^75.6.0" pytest = "^8.2.0" flake8 = "^7.0.0" -pytest-cov = "^5.0.0" +pytest-cov = "^6.0.0" pylint = "^3.2.0" -Sphinx = "^7.3.7" +Sphinx = "^8.1.3" requests = "^2.25.1" -sphinx-rtd-theme = "^2.0.0" +sphinx-rtd-theme = "^3.0.2" papermill = "^2.3.4" [tool.poetry.scripts] diff --git a/tests/test_concise_exception.py b/tests/test_concise_exception.py new file mode 100644 index 00000000..f879b818 --- /dev/null +++ b/tests/test_concise_exception.py @@ -0,0 +1,97 @@ +import pytest +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 diff --git a/tests/test_harmony.py b/tests/test_harmony.py index 9df29b89..08b81845 100644 --- a/tests/test_harmony.py +++ b/tests/test_harmony.py @@ -1,3 +1,4 @@ +from datetime import datetime import json from shutil import rmtree import sys @@ -75,14 +76,17 @@ def test_service_invoke(self): self.assertEqual(item['bbox'], [-4, -3, 4, 3]) self.assertEqual(properties['start_datetime'], '2020-01-01T00:00:00+00:00') self.assertEqual(properties['end_datetime'], '2020-01-05T23:59:59+00:00') - # -- Asset Verification -- data = item['assets']['data'] collection_name = in_message['sources'][0]['collection'] # Sanity checks on metadata - self.assertTrue(data['href'].endswith(f'/{collection_name}_merged.nc4')) - self.assertEqual(data['title'], f'{collection_name}_merged.nc4') + self.assertTrue(data['href'].endswith( + f"{datetime.fromisoformat(properties['end_datetime']).strftime('%Y%m%dT%H%M%SZ')}_{collection_name}_merged.nc4" + )) + self.assertTrue(data['title'].endswith( + f"{datetime.fromisoformat(properties['end_datetime']).strftime('%Y%m%dT%H%M%SZ')}_{collection_name}_merged.nc4" + )) self.assertEqual(data['type'], 'application/x-netcdf4') self.assertEqual(data['roles'], ['data'])