diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 00000000..49bb0597 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[coverage:report] +omit = + */test_* diff --git a/.github/codeql.yml b/.github/codeql.yml new file mode 100644 index 00000000..0f2f9828 --- /dev/null +++ b/.github/codeql.yml @@ -0,0 +1,52 @@ +name: "Code scanning - action" + +on: + push: + pull_request: + schedule: + - cron: '0 19 * * 0' + +jobs: + CodeQL-Build: + + # CodeQL runs on ubuntu-latest and windows-latest + runs-on: ubuntu-latest + + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + # We must fetch at least the immediate parents so that if this is + # a pull request then we can checkout the head. + fetch-depth: 2 + + # If this run was triggered by a pull request event, then checkout + # the head of the pull request instead of the merge commit. + - run: git checkout HEAD^2 + if: ${{ github.event_name == 'pull_request' }} + + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v3 + # Override language selection by uncommenting this and choosing your languages + # with: + # languages: go, javascript, csharp, python, cpp, java + + # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v3 + + # ℹī¸ Command-line programs to run using the OS shell. + # 📚 https://git.io/JvXDl + + # ✏ī¸ If the Autobuild fails above, remove it and uncomment the following three lines + # and modify them (or add more) to build your code if your project + # uses a compiled language + + #- run: | + # make bootstrap + # make release + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v3 diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..1cadfe8e --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,23 @@ +version: 2 +updates: + + # Docker + - package-ecosystem: docker + directory: "/" + schedule: + interval: "monthly" + open-pull-requests-limit: 25 + + # Python + - package-ecosystem: "pip" # See documentation for possible values + directory: "/" # Location of package manifests + schedule: + interval: "monthly" + open-pull-requests-limit: 25 + + # GitHub Actions + - package-ecosystem: "github-actions" + directory: ".github/workflows" + schedule: + interval: "monthly" + open-pull-requests-limit: 25 diff --git a/.github/workflows/manual-build.yml b/.github/workflows/manual-build.yml new file mode 100644 index 00000000..944f9035 --- /dev/null +++ b/.github/workflows/manual-build.yml @@ -0,0 +1,11 @@ +--- +name: Manual Build & Push +on: + workflow_dispatch: +jobs: + build-push: + uses: kbase/.github/.github/workflows/reusable_build-push.yml@main + with: + name: '${{ github.event.repository.name }}-develop' + tags: br-${{ github.ref_name }} + secrets: inherit diff --git a/.github/workflows/pr_build.yml b/.github/workflows/pr_build.yml new file mode 100644 index 00000000..0fa1c464 --- /dev/null +++ b/.github/workflows/pr_build.yml @@ -0,0 +1,43 @@ +--- +name: Pull Request Build, Tag, & Push +on: + pull_request: + branches: + - develop + - main + - master + types: + - opened + - reopened + - synchronize + - closed +jobs: + build-develop-open: + if: github.base_ref == 'develop' && github.event.pull_request.merged == false + uses: kbase/.github/.github/workflows/reusable_build.yml@main + secrets: inherit + build-develop-merge: + if: github.base_ref == 'develop' && github.event.pull_request.merged == true + uses: kbase/.github/.github/workflows/reusable_build-push.yml@main + with: + name: '${{ github.event.repository.name }}-develop' + tags: pr-${{ github.event.number }},latest + secrets: inherit + build-main-open: + if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == false + uses: kbase/.github/.github/workflows/reusable_build-push.yml@main + with: + name: '${{ github.event.repository.name }}' + tags: pr-${{ github.event.number }} + secrets: inherit + build-main-merge: + if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true + uses: kbase/.github/.github/workflows/reusable_build-push.yml@main + with: + name: '${{ github.event.repository.name }}' + tags: pr-${{ github.event.number }},latest-rc + secrets: inherit + trivy-scans: + if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false + uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main + secrets: inherit diff --git a/.github/workflows/release-main.yml b/.github/workflows/release-main.yml new file mode 100644 index 00000000..a2546781 --- /dev/null +++ b/.github/workflows/release-main.yml @@ -0,0 +1,25 @@ +--- +name: Release - Build & Push Image +on: + release: + branches: + - main + - master + types: [ published ] +jobs: + check-source-branch: + uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main + with: + build_branch: '${{ github.event.release.target_commitish }}' + validate-release-tag: + needs: check-source-branch + uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main + with: + release_tag: '${{ github.event.release.tag_name }}' + build-push: + needs: validate-release-tag + uses: kbase/.github/.github/workflows/reusable_build-push.yml@main + with: + name: '${{ github.event.repository.name }}' + tags: '${{ github.event.release.tag_name }},latest' + secrets: inherit diff --git a/.github/workflows/test-release.yml b/.github/workflows/test-release.yml deleted file mode 100644 index b532b461..00000000 --- a/.github/workflows/test-release.yml +++ /dev/null @@ -1,44 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions - -name: Run tests - -on: - push: - branches: [ develop, master ] - pull_request_target: - -jobs: - test: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.7] - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Pip installation - run: python -m pip install --upgrade pip poetry - - name: Poetry installation - run: poetry install - - name: Run tests - run: scripts/run_unit_tests - env: - WORKSPACE_TOKEN: ${{ secrets.WORKSPACE_TOKEN }} - RE_API_TOKEN: ${{ secrets.RE_API_TOKEN }} - -# release: -# runs-on: ubuntu-latest -# needs: test -# # Only run for pushes to develop/master -# # Skip release by putting "skip_docker_build" in the commit message -# if: | -# (github.ref == 'refs/heads/develop' || github.ref == 'refs/heads/master') -# && github.event_name == 'push' -# && !contains(github.event.head_commit.message, 'skip_docker_build') -# steps: -# - name: Docker build and deploy -# run: scripts/docker_deploy diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 00000000..d95fe2b5 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,60 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: Index Runner test + +on: + pull_request: + types: + - opened + - reopened + - synchronize + - ready_for_review + push: + # run workflow when merging to main or develop + branches: + - main + - master + - develop + +jobs: + test: + runs-on: ubuntu-latest + + env: + WORKSPACE_TOKEN: ${{ secrets.WORKSPACE_TOKEN }} + RE_API_TOKEN: ${{ secrets.RE_API_TOKEN }} + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: 3.9.19 + + - name: Pip installation + run: python -m pip install --upgrade pip poetry + + - name: Poetry installation + run: poetry install + + - name: Run unit tests + run: scripts/run_unit_tests + + - name: Run integration tests + run: | + echo "WORKSPACE_TOKEN=$WORKSPACE_TOKEN" > .env + echo "RE_API_TOKEN=$RE_API_TOKEN" >> .env + scripts/run_integration_tests + + - name: Print Docker Compose logs + if: failure() + run: docker compose logs + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v5 + with: + token: ${{ secrets.CODECOV_TOKEN }} + fail_ci_if_error: true diff --git a/CHANGELOG.md b/CHANGELOG.md index 910c9673..dcb50b2f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,8 +6,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## [1.9.21] - 2022-08-28 + +### Added +- Configuration parameter to disable elastic indexing +- Mimimal configuration file for an RE only indexer + +## [1.9.20] - 2022-06-15 + +### Added +- Configuration parameter for max objects in a workspace to skip narrative reindex +- Configuration option to skip narrative reindex for certain workspaces +- Configuration option for poll timeout +- Configuration option to skip narrative reindexing + +## [1.9.19] - 2021-04-19 + ### Fixed - Fixing Samples Releng indexer to work with RE api time-travel. +- Added prefix to default_search alias +- Removed reads_1 from reads alias +- Removed pangenome_orthologfamily from default_search ### Added - adding narrative_config.yaml spec file for separating narrative indexing. diff --git a/Dockerfile b/Dockerfile index bdab5384..a978b0f1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,11 @@ -FROM python:3.7-alpine +FROM python:3.9.19-alpine # Dockerize related args ARG BUILD_DATE ARG VCS_REF ARG BRANCH=develop ENV DOCKERIZE_VERSION v0.6.1 +ENV CRYPTOGRAPHY_DONT_BUILD_RUST 1 # Install dockerize RUN apk --update add --virtual deps curl tar gzip && \ @@ -24,14 +25,21 @@ LABEL org.label-schema.build-date=$BUILD_DATE \ WORKDIR /app # Dependency for confluent-kafka -RUN apk --update add librdkafka librdkafka-dev && ldconfig /usr/lib +RUN apk --update add build-base git cmake bash +RUN git clone --branch v2.6.1 https://github.com/confluentinc/librdkafka.git /tmp/librdkafka +RUN cd /tmp/librdkafka && \ + ./configure && \ + make && \ + make install && \ + ldconfig /usr/lib +RUN rm -rf /tmp/librdkafka # Install dependencies COPY pyproject.toml poetry.lock /app/ -RUN apk --update add --virtual deps python3-dev build-base libffi-dev libressl-dev && \ - pip install --upgrade pip poetry==1.0.9 && \ +RUN apk --update add --virtual deps python3-dev build-base libffi-dev && \ + pip install --upgrade pip poetry==2.1.2 && \ poetry config virtualenvs.create false && \ - poetry install --no-dev --no-interaction --no-ansi && \ + poetry install --no-root --without dev --no-interaction --no-ansi && \ apk del deps # Make the admin tools executable diff --git a/README.md b/README.md index 041a86f1..10df1bbb 100644 --- a/README.md +++ b/README.md @@ -10,13 +10,27 @@ sure to partition the topic to at least the number of running workers. ## Development +### Dependencies + +Note that `docker-compose` 2.3+ is required to run the tests. + +In this project, python packages and dependencies are managed using poetry. To +install the development dependencies, create and activate a python virtual +environment and then run the `poetry install` command. + +### Running the tests + Start the servers: ```sh docker-compose up ``` -Run the tests (servers need not be running, and will be shut down if they are): +To run all the tests the `RE_API_TOKEN` and `WORKSPACE_TOKEN` environment +variables must be set to admin tokens for the relation engine and workspace, +respectively. This project is set up to read a `.env` file, so they may be set +there. The following command will run the tests (servers need not be running, +and will be shut down if they are): ```sh scripts/run_tests @@ -45,6 +59,8 @@ You can set the following env vars: * `SKIP_RELENG` - skip imports into the relation engine (ArangoDB) * `SKIP_FEATURES` - skip any importing or indexing of genome features * `SKIP_INDICES` - comma-separated list of index names that the service will not write into. +* `SKIP_WORKSPACES` - comma-separated list of workspaces that should be skipped +* `MAX_OBJECT_REINDEX` - If the number of objects in the workspace are greater than this value, then the narrative object will not automatically be reindexed. * `ELASTICSEARCH_HOST` - host name of the elasticsearch server to use (do not prepend protocol) * `ELASTICSEARCH_PORT` - port to use for the elasticsearch server * `KBASE_ENDPOINT` - URL of kbase API services (default is "https://ci.kbase.us/services") @@ -80,7 +96,7 @@ Examples: Show command help: `indexer_admin -h` -_Reindex a specific object_ +_Reindex a specific object_ ```sh # Reindex only if the doc does not exist @@ -143,7 +159,7 @@ First, increment the versions found in `VERSION` and in `pyproject.toml`. Then, build the image and push to docker hub with `scripts/docker_deploy`. -### Project anatomy +### Project Anatomy * The main process and entrypoint for the app lives in `./src/index_runner/main.py` * The entrypoint for ES indexing is in `./src/index_runner/es_indexer.py` diff --git a/VERSION b/VERSION index f60acf7e..46b962be 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.9.18 +1.9.21 diff --git a/docker-compose.yaml b/docker-compose.yaml index 5b80b935..a3eb3ace 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,7 +1,8 @@ -version: '3' - # This docker-compose is for developer convenience, not for running in production. +# Uncomment platform: linux/amd64 if you get a "no matching manifest for linux/arm64/v8 in the manifest list entries" error +# when running Docker Compose + services: # For running the python consumers @@ -56,6 +57,7 @@ services: elasticsearch: image: elasticsearch:7.5.0 + # platform: linux/amd64 environment: - "ES_JAVA_OPTS=-Xms512m -Xmx512m" - bootstrap.memory_lock=true @@ -85,6 +87,7 @@ services: # Arangodb server in cluster mode arangodb: image: arangodb:3.5 + # platform: linux/amd64 ports: - "127.0.0.1:8529:8529" # API - "127.0.0.1:8530:8530" # dashboard diff --git a/poetry.lock b/poetry.lock index 45ff56a5..0c143642 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,244 +1,435 @@ -[[package]] -category = "dev" -description = "Disable App Nap on macOS >= 10.9" -marker = "sys_platform == \"darwin\"" -name = "appnope" -optional = false -python-versions = "*" -version = "0.1.2" +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. 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+6,7 @@ authors = ["KBase Team "] license = "MIT" [tool.poetry.dependencies] -python = "^3.7" +python = "3.9.19" kbase_workspace_client = "0.2.1" biopython = "1.77" docker = "4.2.2" @@ -14,13 +14,14 @@ PyYAML = "5.3.1" requests = "2.24.0" beautifulsoup4 = "4.9.1" markdown2 = "2.3.9" -confluent-kafka = "1.5.0" +confluent-kafka = "2.6.1" -[tool.poetry.dev-dependencies] +[tool.poetry.group.dev.dependencies] mypy = "0.782" bandit = "1.6.2" flake8 = "3.8.3" -pytest = "^6.0.1" +pytest = "7.4.0" +pytest-cov = "4.1.0" responses = "^0.11.0" ipython = "^7.18.1" jsonschema = "^3.2.0" diff --git a/scripts/docker_reset b/scripts/docker_reset index 68dae028..9c08f784 100755 --- a/scripts/docker_reset +++ b/scripts/docker_reset @@ -4,5 +4,5 @@ set -euo xtrace # Remove everything in the docker-compose cluster and rebuild -docker-compose down -v --remove-orphans --rmi all -docker-compose build --no-cache +docker compose down -v --remove-orphans --rmi all +docker compose build --no-cache diff --git a/scripts/run_integration_tests b/scripts/run_integration_tests index e1a86bfc..fbfb28fb 100755 --- a/scripts/run_integration_tests +++ b/scripts/run_integration_tests @@ -1,7 +1,7 @@ #!/bin/sh # Run service-dependent slower integration tests set -euo xtrace -docker-compose down && docker-compose up -d +docker compose down && docker compose up -d export PYTHONPATH=. export $(cat tests/test.env | xargs) [ -f .env ] && export $(cat .env | xargs) diff --git a/scripts/run_unit_tests b/scripts/run_unit_tests index 4f038828..f611e789 100755 --- a/scripts/run_unit_tests +++ b/scripts/run_unit_tests @@ -9,4 +9,5 @@ export PYTHONPATH=. export $(cat tests/test.env | xargs) # Allow users to set test args args=${@:-"tests/unit"} -poetry run pytest $args +scripts/lint +poetry run pytest --cov=. --cov-report=term --cov-report=xml $args diff --git a/spec/re_config.yaml b/spec/re_config.yaml new file mode 100644 index 00000000..1a6d7172 --- /dev/null +++ b/spec/re_config.yaml @@ -0,0 +1,18 @@ +# Mapping of KBase type names to index names +ws_type_to_indexes: {} + +# SDK apps used for indexing, map from type_module.type_name -> {'sdk_func': _, 'sdk_app': _, 'sdk_version': +sdk_indexer_apps: {} + +ws_subobjects: [] + +latest_versions: {} +global_mappings: {} +aliases: {} +mappings: {} + +# Types to always avoid indexing or importing +ws_type_blacklist: [] + + + diff --git a/src/index_runner/es_indexer.py b/src/index_runner/es_indexer.py index 1f097ef7..8846df1a 100644 --- a/src/index_runner/es_indexer.py +++ b/src/index_runner/es_indexer.py @@ -188,7 +188,7 @@ def _init_generic_index(msg): mappings = {**_GLOBAL_MAPPINGS['ws_auth'], **_GLOBAL_MAPPINGS['ws_object']} _init_index(index_name, mappings) # Update the 'default_search' alias to include this index - _create_alias(_DEFAULT_SEARCH_ALIAS, f"{_PREFIX}.{index_name}") + _create_alias(f"{_PREFIX}.{_DEFAULT_SEARCH_ALIAS}", f"{_PREFIX}.{index_name}") def _write_to_elastic(data): diff --git a/src/index_runner/main.py b/src/index_runner/main.py index 3df11a74..6ae8ae22 100644 --- a/src/index_runner/main.py +++ b/src/index_runner/main.py @@ -41,13 +41,20 @@ def _handle_msg(msg): logger.warning(f"Type {objtype} is in SKIP_TYPES, skipping") return if event_type in ['REINDEX', 'NEW_VERSION', 'COPY_OBJECT', 'RENAME_OBJECT']: + # Skip any workspaces in the skip list + wsid = msg['wsid'] + if wsid in config()['skip_workspaces']: + logger.warning(f"Workspace {wsid} in skip list, skipping") + return # Index a single workspace object obj = _fetch_obj_data(msg) ws_info = _fetch_ws_info(msg) - _reindex_narrative(obj, ws_info) + if not config()['skip_narrative_reindex']: + _reindex_narrative(obj, ws_info) if not config()['skip_releng']: releng_importer.run_importer(obj, ws_info, msg) - es_indexer.run_indexer(obj, ws_info, msg) + if not config()['skip_es']: + es_indexer.run_indexer(obj, ws_info, msg) elif event_type == 'REINDEX_WS' or event_type == 'CLONE_WORKSPACE': # Reindex all objects in a workspace, overwriting existing data for objinfo in config()['ws_client'].generate_obj_infos(msg['wsid'], admin=True): @@ -73,29 +80,34 @@ def _handle_msg(msg): ws_info = _fetch_ws_info(msg) if re_required: releng_importer.run_importer(obj, ws_info, msg) - if es_required: + if es_required and not config()['skip_es']: es_indexer.run_indexer(obj, ws_info, msg) elif event_type == 'OBJECT_DELETE_STATE_CHANGE': # Delete the object on RE and ES. Synchronous for now. - es_indexer.delete_obj(msg) + if not config()['skip_es']: + es_indexer.delete_obj(msg) if not config()['skip_releng']: releng_importer.delete_obj(msg) elif event_type == 'WORKSPACE_DELETE_STATE_CHANGE': # Delete everything in RE and ES under this workspace - es_indexer.delete_ws(msg) + if not config()['skip_es']: + es_indexer.delete_ws(msg) if not config()['skip_releng']: releng_importer.delete_ws(msg) elif event_type == 'SET_GLOBAL_PERMISSION': # Set the `is_public` permissions for a workspace - es_indexer.set_perms(msg) + if not config()['skip_es']: + es_indexer.set_perms(msg) if not config()['skip_releng']: releng_importer.set_perms(msg) elif event_type == 'SET_PERMISSION': # Share the narrative with users - es_indexer.set_user_perms(msg) + if not config()['skip_es']: + es_indexer.set_user_perms(msg) elif event_type == 'RELOAD_ELASTIC_ALIASES': # Reload aliases on ES from the global config file - es_indexer.reload_aliases() + if not config()['skip_es']: + es_indexer.reload_aliases() else: logger.warning(f"Unrecognized event {event_type}.") @@ -154,6 +166,11 @@ def _fetch_ws_info(msg): def _reindex_narrative(obj, ws_info: dict) -> None: + # Skip narrative reindex if there are too many objects + if ws_info[4] > config()['max_object_reindex']: + m = "Skipping narrative reindex for %d (too many objects)" % (ws_info[0]) + logger.info(m) + return obj_type = obj['info'][2] if 'Narrative' in obj_type: return @@ -227,9 +244,10 @@ def main(): os.remove(config()['proc_ready_path']) # Wait for dependency services (ES and RE) to be live wait_for_dependencies(timeout=180) - # Database initialization - es_indexer.init_indexes() - es_indexer.reload_aliases() + if not config()['skip_es']: + # Database initialization + es_indexer.init_indexes() + es_indexer.reload_aliases() # Touch a temp file indicating the daemon is ready with open(config()['proc_ready_path'], 'w') as fd: fd.write('') diff --git a/src/index_runner/releng/import_obj.py b/src/index_runner/releng/import_obj.py index 0da42b76..0696acbc 100644 --- a/src/index_runner/releng/import_obj.py +++ b/src/index_runner/releng/import_obj.py @@ -53,6 +53,7 @@ def import_object(obj, ws_info): # this could use a lot of memory. There's a bunch of code in the workspace for # dealing with this situation, but that'd have to be ported to Python and it's pretty # complex, so YAGNI for now. + logger.debug(f'Using releng indexer for "{type_}" workspace type for ws_object with key {obj_key}') resp = config()['ws_client'].admin_req('getObjects', { 'objects': [{ 'ref': obj_ver_key.replace(':', '/'), diff --git a/src/index_runner/releng/samples.py b/src/index_runner/releng/samples.py index 8fee28ec..a741f496 100644 --- a/src/index_runner/releng/samples.py +++ b/src/index_runner/releng/samples.py @@ -16,7 +16,6 @@ from src.utils.sample_utils import get_sample as _get_sample from src.utils.re_client import MAX_ADB_INTEGER as _MAX_ADB_INTEGER - # EXTREMELY HACKY FOR NOW. SHOULD BE RETRIEVED (?) FROM THE SAMPLE_SERVICE SAMPLE_COLL = 'samples_sample' SAMPLE_VER_COLL = 'samples_version' @@ -122,8 +121,8 @@ def _generate_link_information(sample: dict, sample_version_uuid: str, edges: li # ontology_doc_id contains the source ontology ontology_collection, ontology_doc_key = ontology_doc_id.split('/') edge = { - "from": node_doc_id, - "to": ontology_doc_id, + "_from": node_doc_id, + "_to": ontology_doc_id, "_key": _clean_key(f"{node_uuid}_{ontology_doc_key}"), # placeholder _key for now. "createdby": "kbase_RE_indexer", # Should be owner of sample (?) "expired": _MAX_ADB_INTEGER, diff --git a/src/utils/config.py b/src/utils/config.py index af9feb46..6a5b4dbc 100644 --- a/src/utils/config.py +++ b/src/utils/config.py @@ -78,12 +78,16 @@ def reload(self, force_reload=False): ws_token = os.environ['WORKSPACE_TOKEN'] es_host = os.environ.get("ELASTICSEARCH_HOST", 'elasticsearch') es_port = os.environ.get("ELASTICSEARCH_PORT", 9200) + poll_timeout = int(os.environ.get("POLL_TIMEOUT", "600000")) kbase_endpoint = os.environ.get( 'KBASE_ENDPOINT', 'https://ci.kbase.us/services').strip('/') workspace_url = os.environ.get('WS_URL', kbase_endpoint + '/ws') catalog_url = os.environ.get('CATALOG_URL', kbase_endpoint + '/catalog') re_api_url = os.environ.get('RE_URL', kbase_endpoint + '/relation_engine_api').strip('/') sample_service_url = os.environ.get("SAMPLE_SERVICE_URL") + skip_narrative_reindex = False + if os.environ.get("SKIP_NARRATIVE_REINDEX"): + skip_narrative_reindex = True if sample_service_url is None: service_wizard_url = os.environ.get('SW_URL', kbase_endpoint + '/service_wizard').strip('/') sample_service_release = os.environ.get('SAMPLE_SERVICE_RELEASE', 'dev') @@ -96,6 +100,11 @@ def reload(self, force_reload=False): sample_ontology_config = _fetch_global_config(sample_ontology_config_url) global_config = _fetch_global_config(config_url) skip_indices = _get_comma_delimited_env('SKIP_INDICES') + skip_workspaces = set() + if 'SKIP_WORKSPACES' in os.environ: + for ws in _get_comma_delimited_env('SKIP_WORKSPACES'): + skip_workspaces.add(int(ws)) + max_object_reindex = int(os.environ.get('MAX_OBJECT_REINDEX', '500')) allow_indices = _get_comma_delimited_env('ALLOW_INDICES') # Use a tempfile to indicate that the service is done booting up proc_ready_path = '/tmp/IR_READY' # nosec @@ -108,8 +117,13 @@ def reload(self, force_reload=False): self._cfg = { 'service_wizard_url': service_wizard_url, 'skip_releng': os.environ.get('SKIP_RELENG'), + 'skip_es': os.environ.get('SKIP_ES'), 'skip_features': os.environ.get('SKIP_FEATURES'), 'skip_indices': skip_indices, + 'skip_workspaces': skip_workspaces, + 'max_object_reindex': max_object_reindex, + 'poll_timeout': poll_timeout, + 'skip_narrative_reindex': skip_narrative_reindex, 'allow_indices': allow_indices, 'global': global_config, 'global_config_url': config_url, diff --git a/src/utils/kafka.py b/src/utils/kafka.py index 714f3929..7979eb5b 100644 --- a/src/utils/kafka.py +++ b/src/utils/kafka.py @@ -15,15 +15,17 @@ def init_consumer(topics: List[str]) -> Consumer: """ Initialize a Kafka consumer instance """ + conf = config() consumer = Consumer({ - 'bootstrap.servers': config()['kafka_server'], - 'group.id': config()['kafka_clientgroup'], + 'bootstrap.servers': conf['kafka_server'], + 'group.id': conf['kafka_clientgroup'], 'auto.offset.reset': 'earliest', + 'max.poll.interval.ms': conf['poll_timeout'], 'enable.auto.commit': False }) logger.info(f"Subscribing to: {topics}") - logger.info(f"Client group: {config()['kafka_clientgroup']}") - logger.info(f"Kafka server: {config()['kafka_server']}") + logger.info(f"Client group: {conf['kafka_clientgroup']}") + logger.info(f"Kafka server: {conf['kafka_server']}") consumer.subscribe(topics) return consumer diff --git a/tests/unit/index_runner/releng/test_samples.py b/tests/unit/index_runner/releng/test_samples.py index 0410442e..07e3e29b 100644 --- a/tests/unit/index_runner/releng/test_samples.py +++ b/tests/unit/index_runner/releng/test_samples.py @@ -29,6 +29,6 @@ def test_generate_sample_set_edges(): assert len(edges) == 2 node_id = _hash("node_id") for e in edges: - assert "from" in e - assert "to" in e - assert e["from"] == f"samples_nodes/sample-uuid_sample-version-uuid_{node_id}" + assert "_from" in e + assert "_to" in e + assert e["_from"] == f"samples_nodes/sample-uuid_sample-version-uuid_{node_id}" diff --git a/tests/unit/index_runner/test_main.py b/tests/unit/index_runner/test_main.py index 4ff2e662..6ff75c37 100644 --- a/tests/unit/index_runner/test_main.py +++ b/tests/unit/index_runner/test_main.py @@ -2,7 +2,7 @@ import responses from tests.helpers import set_env -from src.index_runner.main import _handle_msg +from src.index_runner.main import _handle_msg, _reindex_narrative from src.utils.config import config # Allow requests to the service wizard (which happens in config) @@ -52,6 +52,27 @@ def test_handle_msg_allow_types2(): assert str(ctx.value) == "Missing 'evtype' in event: {'objtype': 'xyz'}" +def test_skip_workspace(): + """ + Test that an event from a workspace in skip_workspaces is skipped. + """ + with set_env(SKIP_WORKSPACES='123,124'): + config(force_reload=True) + res = _handle_msg({'objtype': 'abc', 'evtype': 'REINDEX', 'wsid': 123}) + assert res is None + + +def test_skip_reindex(): + """ + Test that a large workspace doesn't cause a reindex + """ + ws_info = [123, 'auser:narrative_1653154144334', + 'auser', '2022-06-28T16:02:17+0000', 1000, + 'n', 'n', 'unlocked', {}] + res = _reindex_narrative(None, ws_info) + assert res is None + + @responses.activate def test_handle_msg_no_objtype(): """Valid test path for filtering by type when no `objtype` field is diff --git a/tests/unit/test_config.py b/tests/unit/test_config.py new file mode 100644 index 00000000..269a4d1e --- /dev/null +++ b/tests/unit/test_config.py @@ -0,0 +1,35 @@ +from src.utils.config import config +from tests.helpers import set_env +import os + +""" +Add some minimal tests for the config object. +More should be added to this. +""" + + +def test_config_defaults(): + if "WORKSPACE_TOKEN" not in os.environ: + os.environ["WORKSPACE_TOKEN"] = "bogus" + if "RE_API_TOKEN" not in os.environ: + os.environ["RE_API_TOKEN"] = "bogus" + assert config()["max_object_reindex"] == 500 + assert config()["skip_workspaces"] == set() + + +def test_max_object_reindex(): + assert config()["max_object_reindex"] == 500 + # Force reload + with set_env(MAX_OBJECT_REINDEX="1000"): + config()._cfg['last_config_reload'] = 0 + config().reload() + assert config()["max_object_reindex"] == 1000 + + +def test_skip_es(): + assert config()["skip_es"] is None + # Force reload + with set_env(SKIP_ES='1'): + config()._cfg['last_config_reload'] = 0 + config().reload() + assert config()["skip_es"] == "1" diff --git a/tests/wait_for_deps.py b/tests/wait_for_deps.py index c9501d15..a5357ce4 100644 --- a/tests/wait_for_deps.py +++ b/tests/wait_for_deps.py @@ -11,7 +11,7 @@ if __name__ == '__main__': tmp_ready_path = config()['proc_ready_path'] - cmd = ["docker-compose", "exec", "app", "ls", tmp_ready_path] + cmd = ["docker", "compose", "exec", "app", "ls", tmp_ready_path] timeout = 180 start = time.time() while True: