diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e245323..c0298b5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,18 +5,20 @@ on: branches: - main pull_request: - branches: - - "**" - paths-ignore: - - "docs/**" - types: [ready_for_review] + branches: + - "**" + paths-ignore: + - "docs/**" + types: + - ready_for_review + - synchronize jobs: pre-commit: strategy: matrix: os: [ubuntu-latest] - python-version: ['3.9'] + python-version: ["3.10"] runs-on: ${{ matrix.os }} steps: - @@ -34,7 +36,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: ['3.9'] + python-version: ["3.10"] runs-on: ${{ matrix.os }} needs: pre-commit steps: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 736d84b..600712a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,98 +1,99 @@ repos: -- hooks: - - args: - - --multi-line=3 - - --trailing-comma - - --force-grid-wrap=0 - - --use-parentheses - - --line-width=88 - - --ensure-newline-before-comments - id: isort - repo: https://github.com/pycqa/isort - rev: 5.12.0 -- hooks: - - args: - - --max-line-length=89 - - --max-complexity=15 - id: flake8 - repo: https://github.com/pycqa/flake8 - rev: 6.1.0 -- hooks: - - args: - - --py36-plus - id: pyupgrade - repo: https://github.com/asottile/pyupgrade - rev: v3.13.0 -- hooks: - - id: black - repo: https://github.com/psf/black - rev: 23.9.1 -- hooks: - - additional_dependencies: - - types-attrs - - types-requests - - types-setuptools - - types-PyYAML - - types-toml - args: - - --ignore-missing-imports - - --no-implicit-optional - id: mypy - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.5.1 -- hooks: - - args: - - --convention=google - - --add-ignore=D104 - id: pydocstyle - repo: https://github.com/pycqa/pydocstyle - rev: 6.3.0 -- hooks: - - id: blacken-docs - repo: https://github.com/asottile/blacken-docs - rev: 1.16.0 -- hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: debug-statements - - id: check-case-conflict - - id: check-json - - id: check-added-large-files - - id: check-yaml - - id: mixed-line-ending - - id: check-toml - - id: pretty-format-json - - id: check-docstring-first - - id: check-symlinks - - id: detect-private-key - - id: pretty-format-json - args: - - --autofix - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 -- hooks: - - args: - - -iii - - -lll - id: bandit - repo: https://github.com/PyCQA/bandit - rev: 1.7.5 -- hooks: - - additional_dependencies: - - radon - args: - - cc - - --min=C - - --total-average - entry: radon - id: radon - language: python - name: radon - verbose: true - repo: local -- hooks: - - id: commitizen - stages: - - commit-msg - repo: https://github.com/commitizen-tools/commitizen - rev: 3.10.0 + - hooks: + - args: + - --multi-line=3 + - --trailing-comma + - --force-grid-wrap=0 + - --use-parentheses + - --line-width=88 + - --ensure-newline-before-comments + id: isort + repo: https://github.com/pycqa/isort + rev: 5.13.2 + - hooks: + - args: + - --max-line-length=89 + - --max-complexity=15 + - --extend-ignore=E203 + id: flake8 + repo: https://github.com/pycqa/flake8 + rev: 7.0.0 + - hooks: + - args: + - --py36-plus + id: pyupgrade + repo: https://github.com/asottile/pyupgrade + rev: v3.15.0 + - hooks: + - id: black + repo: https://github.com/psf/black + rev: 23.9.1 + - hooks: + - additional_dependencies: + - types-attrs + - types-requests + - types-setuptools + - types-PyYAML + - types-toml + args: + - --ignore-missing-imports + - --no-implicit-optional + id: mypy + repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.8.0 + - hooks: + - args: + - --convention=google + - --add-ignore=D104 + id: pydocstyle + repo: https://github.com/pycqa/pydocstyle + rev: 6.3.0 + - hooks: + - id: blacken-docs + repo: https://github.com/asottile/blacken-docs + rev: 1.16.0 + - hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: debug-statements + - id: check-case-conflict + - id: check-json + - id: check-added-large-files + - id: check-yaml + - id: mixed-line-ending + - id: check-toml + - id: pretty-format-json + - id: check-docstring-first + - id: check-symlinks + - id: detect-private-key + - id: pretty-format-json + args: + - --autofix + repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + - hooks: + - args: + - -iii + - -lll + id: bandit + repo: https://github.com/PyCQA/bandit + rev: 1.7.6 + - hooks: + - additional_dependencies: + - radon + args: + - cc + - --min=C + - --total-average + entry: radon + id: radon + language: python + name: radon + verbose: true + repo: local + - hooks: + - id: commitizen + stages: + - commit-msg + repo: https://github.com/commitizen-tools/commitizen + rev: v3.13.0 diff --git a/docs/workspaces.md b/docs/workspaces.md index 6033e5d..5f965ae 100644 --- a/docs/workspaces.md +++ b/docs/workspaces.md @@ -31,9 +31,11 @@ To remove an active workspace, ```bash workflow workspace rm ``` + This will only remove the active workspace, i.e. `~/.workflow/workspaces/active.yml`. !!! Important + Running workflow without a workspace set will result in an runtime error. In order to purge all workspaces, from `~/.workflow/workspaces/` run: @@ -44,7 +46,7 @@ In order to purge all workspaces, from `~/.workflow/workspaces/` run: ### Configuration for container images -In order to run workflow, pre-configured from container images, it is recommended to set the `workflow set workspace` command during the container build process. For example, in a Dockerfile: +In order to run workflow, pre-configured from container images, it is recommended to set the `workflow set workspace` command during the container build process. For example, in a Dockerfile: ```dockerfile FROM python:3.8-slim-buster @@ -53,3 +55,151 @@ In order to run workflow, pre-configured from container images, it is recommende pip install workflow && \ workflow workspace set development ``` + +## Workspace YAML format + +### `workspace` + +This key states the name of the workspace. + + ```yaml + workspace: "test-workspace" + ``` + +### `sites` + +Under the 'sites' key is where a list of strings naming the sites that +are allowed when running Workflow. Eg: + + ```yaml + sites: + - local + ``` + +### `archive` + +The 'archive' key describes the storage sites that are available. Valid +keys are: + +- `mounts`, which should contain a key for every valid site listed under + `sites` giving its root mount point. + + ```yaml + archive: + mounts: + local: "./" + ``` + +### `http` + +The `http` key contains the configuration for requests that utilise http. +It is here that we set the base URLs for Workflow's dependant services. + +- `baseurls`, this should contain a URL for each of the six services that + Workflow is able to use. These comprise: + + - Buckets database + - Results database + - Pipelines API + - Products API + - Loki logs + - MinIO object storage + + An example of this section of the YAML file: + + ```yaml + http: + baseurls: + buckets: http://localhost:8001 + results: http://localhost:8002 + pipelines: http://localhost:8003 + products: http://localhost:8004 + minio: http://localhost:8005 + loki: http://localhost:8005/loki/api/v1/push + ``` + +### `config` + +- `archive` + + - `results`, this key enables or disables the functionality to copy Work + entries across to the Results database upon their completion. Valid values + are either: + + ```yaml + # To enable + results: true + # To disable + results: false + + ``` + + - `plots`, this sets the archiving methods and storage type for plots produced + when using Workflow. It has the following keys: + + - `methods`, this is a list that sets the methods enabled by the workspace admin + these can be a including any of the following: `bypass`, `move`, `copy`, `delete`. + - `storage`, this tells Workflow what storage type it will use to archive + the plots, which can be either: `s3`, `posix`, or `http` (currently only + has place-holding code). + + ```yaml + plots: + methods: ["move", "delete"] + storage: "s3" + ``` + + - `products`, this sets the archiving methods and storage type for the products + produced. It has the same keys as `plots`, above, and those have the same options. + + - `methods`, same as above. + - `storage`, same as above. + + ```yaml + products: + methods: ["bypass", "copy"] + storage: "posix" + ``` + + - `permissions`, this is used by the archiver to determine how to set the permissions + for each storage type. Although, 's3' is included here, MinIO handles permissions + internally. + + - `s3` + - `user` + - `group` + - `posix` + + - `command`, this is an f-string template that defines the command that you wish + to use to set the directory permissions. + - `user`, the user to use in the permissions command. + - `group`, the group to use in the permissions command. + + ```yaml + posix: + group: "chime-frb-rw" + command: "setfacl -R m g:{group}:rw {path}" + ``` + +Below is an example of the `config` section of the workspace YAML. + + ```yaml + config: + archive: + results: true + plots: + methods: ["move", "delete"] + storage: "s3" + products: + methods: ["bypass", "copy"] + storage: "posix" + permissions: + s3: + user: "user1" + group: "group1" + posix: + group: "group1" + command: "setfacl -R -m g:{group}:r {path}" + ``` + +- `slack`, WIP; to be implemented. diff --git a/poetry.lock b/poetry.lock index fe4ed28..6eb5d4b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,26 +1,50 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. - [[package]] name = "annotated-types" version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" +category = "main" optional = false python-versions = ">=3.8" -files = [ - {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, - {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, -] + +[[package]] +name = "argon2-cffi" +version = "23.1.0" +description = "Argon2 for Python" +category = "main" +optional = false +python-versions = ">=3.7" + +[package.dependencies] +argon2-cffi-bindings = "*" + +[package.extras] +dev = ["argon2-cffi[tests,typing]", "tox (>4)"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"] +tests = ["hypothesis", "pytest"] +typing = ["mypy"] + +[[package]] +name = "argon2-cffi-bindings" +version = "21.2.0" +description = "Low-level CFFI bindings for Argon2" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +cffi = ">=1.0.1" + +[package.extras] +dev = ["cogapp", "pre-commit", "pytest", "wheel"] +tests = ["pytest"] [[package]] name = "babel" version = "2.14.0" description = "Internationalization utilities" +category = "dev" optional = false python-versions = ">=3.7" -files = [ - {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, - {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, -] [package.extras] dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] @@ -29,133 +53,44 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] name = "certifi" version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" -files = [ - {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"}, - {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"}, -] + +[[package]] +name = "cffi" +version = "1.16.0" +description = "Foreign Function Interface for Python calling C code." +category = "main" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +pycparser = "*" [[package]] name = "cfgv" version = "3.4.0" description = "Validate configuration and produce human readable error messages." +category = "dev" optional = false python-versions = ">=3.8" -files = [ - {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, - {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, -] [[package]] name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. 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"pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] - -[metadata] -lock-version = "2.0" -python-versions = "^3.9" -content-hash = "97ea4a825805bad06407b40300eb84f87495894f52ae3baf4860cadc05a4ca24" diff --git a/pyproject.toml b/pyproject.toml index 020f8e1..355782f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,8 @@ toml = "^0.10" rich = "^13.4" mergedeep = "^1.3" pydantic-settings = "^2.0" +minio = "^7.2.3" +python-logging-loki = "^0.3.1" [tool.poetry.group.dev.dependencies] mypy = "*" @@ -28,6 +30,7 @@ types-requests = "*" types-toml = "*" types-setuptools = "*" types-pyyaml = "*" +pytest-env = "^1.1.3" [tool.poetry.group.docs.dependencies] diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..67e3559 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,5 @@ +[pytest] +env = + WORKFLOW_S3_ENDPOINT=play.min.io + WORKFLOW_S3_ACCESS_KEY=Q3AM3UQ867SPQQA43P2F + WORKFLOW_S3_SECRET_KEY=zuf+tfteSlswRu7BJ86wekitnifILbZam1KYY3TG diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..41a4078 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,15 @@ +"""pytest configuration file.""" +from click.testing import CliRunner + +from workflow.cli.main import cli as workflow + + +def pytest_configure(config): + """Initailize pytest configuration. + + Allows plugins and conftest files to perform initial configuration. + This hook is called for every plugin and initial conftest + file after command line options have been parsed. + """ + runner = CliRunner() + runner.invoke(workflow, ["workspace", "set", "development"]) diff --git a/tests/test_archive.py b/tests/test_archive.py new file mode 100644 index 0000000..b272b7e --- /dev/null +++ b/tests/test_archive.py @@ -0,0 +1,196 @@ +"""Test the archive module.""" + +import logging +import os +import shutil +from pathlib import Path + +import pytest +from pydantic import ValidationError + +from workflow.definitions.work import Work +from workflow.lifecycle.archive import http, posix, run, s3 +from workflow.utils import read + +WORKSPACE = read.workspace("sample-test") + + +@pytest.fixture(scope="module") +def directory(): + """Create a temporary directory. + + Yields: + directory (Path): Path to temporary directory. + """ + directory = Path("tmp_test") + directory.mkdir(exist_ok=True) + yield directory + shutil.rmtree(directory) + + +@pytest.fixture +def work(): + """Return a Work instance.""" + test_plot = Path("test_plot.txt") + test_product = Path("test_product.txt") + test_plot.touch() + test_product.touch() + yield Work( + user="tester", + site="local", + pipeline="test-pipeline", + id="pytest", + plots=[test_plot.as_posix()], + products=[test_product.as_posix()], + ) + test_plot.unlink(missing_ok=True) + test_product.unlink(missing_ok=True) + + +def test_s3_env_vars_set(): + """Test the environment for S3 vars.""" + assert os.getenv("WORKFLOW_S3_ENDPOINT") == "play.min.io" + assert os.getenv("WORKFLOW_S3_ACCESS_KEY") == "Q3AM3UQ867SPQQA43P2F" + assert ( + os.getenv("WORKFLOW_S3_SECRET_KEY") + == "zuf+tfteSlswRu7BJ86wekitnifILbZam1KYY3TG" + ) + + +def test_successful_run_archive(work): + """Test the run function.""" + run(work, WORKSPACE) + + +def test_bad_method_run_archive(caplog, work, workspace=WORKSPACE): + """Test the run function.""" + with pytest.raises(ValidationError): + work.config.archive.products = "bad_method" + work.config.archive.plots = "bad_method" + run(work, workspace) + + +def test_excluded_method_run_archive(caplog, work, workspace=WORKSPACE): + """Test the run function.""" + work.config.archive.products = "bypass" + work.config.archive.plots = "bypass" + workspace["config"]["archive"]["products"]["methods"] = ["copy"] + workspace["config"]["archive"]["plots"]["methods"] = ["copy"] + with caplog.at_level(logging.WARNING): + run(work, workspace) + assert ( + f"Archive method {work.config.archive.products} not allowed for products by workspace." # noqa: E501 + in caplog.text + ) + assert ( + f"Archive method {work.config.archive.plots} not allowed for plots by workspace." # noqa: E501 + in caplog.text + ) + + +def test_storage_unset_run_archive(caplog, work, workspace=WORKSPACE): + """Test the run function.""" + workspace["config"]["archive"]["products"]["storage"] = None + workspace["config"]["archive"]["plots"]["storage"] = None + with caplog.at_level(logging.WARNING): + run(work, workspace) + assert "storage has not been set for products in workspace." in caplog.text + assert "storage has not been set for plots in workspace." in caplog.text + + +class TestS3: + """Test S3 archive methods.""" + + def test_s3_bypass(self): + """Test the bypass method.""" + assert s3.bypass(Path("none"), []) is True + + def test_s3_copy(self, work): + """Test the copy method.""" + file = work.plots[0] + path = Path("workflow/testing/s3/method/copy") + result = s3.copy(path, [file]) + assert result is True + + def test_s3_delete(self): + """Test the delete method.""" + with pytest.raises(NotImplementedError): + s3.delete(Path("none"), []) + + def test_s3_move(self, work): + """Test the move method.""" + file = work.plots[0] + path = Path("workflow/testing/s3/method/move") + result = s3.move(path, [file]) + assert result is True + + def test_s3_permissions(self): + """Test the permissions method.""" + with pytest.raises(NotImplementedError): + s3.permissions(Path("none"), []) + + +class TestPosix: + """Test POSIX archive methods.""" + + def test_posix_bypass(self): + """Test the bypass method.""" + assert posix.bypass(Path("none"), []) is True + + def test_posix_copy(self, work, directory): + """Test the copy method.""" + file = work.plots[0] + path = directory / "posix" / "method" / "copy" + result = posix.copy(path, [file]) + assert result is True + assert (path / file).exists() + + def test_posix_delete(self, work, directory): + """Test the delete method.""" + file = work.plots[0] + path = directory / "posix" / "method" / "delete" + result = posix.delete(path, work.plots) + assert result is True + assert not Path(file).exists() + assert len(work.plots) == 0 + + def test_posix_move(self, work, directory): + """Test the move method.""" + file = work.plots[0] + path = directory / "posix" / "method" / "move" + result = posix.move(path, [file]) + assert result is True + assert (path / file).exists() + assert not Path(file).exists() + + def test_posix_permissions(self): + """Test the permissions method.""" + pass + + +class TestHttp: + """Test HTTP archive methods.""" + + def test_http_bypass(self): + """Test the bypass method.""" + assert http.bypass(Path("none"), []) is True + + def test_http_copy(self): + """Test the copy method.""" + with pytest.raises(NotImplementedError): + http.copy(Path("none"), []) + + def test_http_delete(self): + """Test the delete method.""" + with pytest.raises(NotImplementedError): + http.delete(Path("none"), []) + + def test_http_move(self): + """Test the move method.""" + with pytest.raises(NotImplementedError): + http.move(Path("none"), []) + + def test_http_permissions(self): + """Test the permissions method.""" + with pytest.raises(NotImplementedError): + http.permissions(Path("none"), []) diff --git a/workflow/cli/run.py b/workflow/cli/run.py index e7da20e..81bbd8d 100644 --- a/workflow/cli/run.py +++ b/workflow/cli/run.py @@ -9,16 +9,13 @@ import click import requests - -# from chime_frb_api.configs import LOKI_URLS, PRODUCTS_URLS, WORKFLOW_URLS -# from chime_frb_api.utils import loki from rich.console import Console from workflow import DEFAULT_WORKSPACE_PATH from workflow.definitions.work import Work from workflow.lifecycle import archive, container, execute, validate from workflow.utils import read as reader -from workflow.utils.logger import get_logger, set_tag, unset_tag +from workflow.utils.logger import add_loki_handler, get_logger, set_tag, unset_tag logger = get_logger("workflow.cli") @@ -26,7 +23,8 @@ @click.command("run", short_help="Perform work.") @click.argument("bucket", type=str, required=True) @click.option( - "-f" "--function", + "-f", + "--function", type=str, required=False, default=None, @@ -157,7 +155,7 @@ def run( "[bold]Configuration Checks [/bold]", extra=dict(markup=True, color="green"), ) - loki_status = loki.add_handler(logger, site, bucket, loki_url) + loki_status = add_loki_handler(logger, loki_url, config) logger.info(f"Loki Logs: {'✅' if loki_status else '❌'}") try: @@ -189,7 +187,9 @@ def run( refresh_per_second=1, speed=1 / slowdown, ): - lifecycle(bucket, function, lives, sleep, site, tags, parent, buckets_url) + lifecycle( + bucket, function, lives, sleep, site, tags, parent, buckets_url, config + ) except Exception as error: logger.exception(error) finally: @@ -208,6 +208,7 @@ def lifecycle( tags: List[str], parent: Optional[str], base_url: str, + config: Dict[str, Any], ): """Run the workflow lifecycle.""" # Start the exit event @@ -225,7 +226,7 @@ def quit(signo: int, _: Any): # Run the lifecycle until the exit event is set or the lifetime is reached while lifetime != 0 and not exit.is_set(): - attempt(bucket, function, base_url, site, tags, parent) + attempt(bucket, function, base_url, site, tags, parent, config) lifetime -= 1 logger.debug(f"sleeping: {sleep_time}s") exit.wait(sleep_time) @@ -239,6 +240,7 @@ def attempt( site: str, tags: Optional[List[str]], parent: Optional[str], + config: Dict[str, Any], ) -> bool: """Attempt to perform work. @@ -298,22 +300,20 @@ def attempt( work = execute.command(command, work) if int(work.timeout) + int(work.start) < time.time(): # type: ignore raise TimeoutError("work timed out") - archive.run(work) + archive.run(work, config) status = True except Exception as error: logger.exception(error) work.status = "failure" # type: ignore finally: if work: + product_url = config.get("http", {}).get("baseurls", {}).get("products", "") if any(work.notify.slack.dict().values()) and work.products: work.products = [ - f"<{str(PRODUCTS_URLS[site])}{product}|{product}>" - for product in work.products + f"<{product_url}{product}|{product}>" for product in work.products ] if any(work.notify.slack.dict().values()) and work.plots: - work.plots = [ - f"<{str(PRODUCTS_URLS[site])}{plot}|{plot}>" for plot in work.plots - ] + work.plots = [f"<{product_url}{plot}|{plot}>" for plot in work.plots] work.update(**kwargs) # type: ignore logger.info("work completed: ✅") unset_tag() diff --git a/workflow/daemons/transfer.py b/workflow/daemons/transfer.py index 12b0ce9..bca2f65 100644 --- a/workflow/daemons/transfer.py +++ b/workflow/daemons/transfer.py @@ -4,11 +4,12 @@ import click +from workflow import DEFAULT_WORKSPACE_PATH from workflow.http.buckets import Buckets from workflow.http.results import Results -from workflow.utils.logger import get_logger +from workflow.utils import logger, read -log = get_logger("workflow.daemons.transfer") +log = logger.get_logger("workflow.daemons.transfer") def deposit_work_to_results( @@ -115,6 +116,12 @@ def transfer(test_flag: bool, buckets: Buckets, results: Results) -> Dict[str, A Returns: Dict[str, Any]: Transfer status. """ + results_workspace_config = ( + read.workspace(DEFAULT_WORKSPACE_PATH.as_posix()) + .get("config", {}) + .get("archive", {}) + .get("results", None) + ) transfer_status: Dict[str, Any] = {} # 1. Transfer successful Work # TODO: decide projection fields @@ -128,11 +135,12 @@ def transfer(test_flag: bool, buckets: Buckets, results: Results) -> Dict[str, A work for work in successful_work if work["config"]["archive"]["results"] is False + and not results_workspace_config ] successful_work_to_transfer = [ work for work in successful_work - if work["config"]["archive"]["results"] is True + if work["config"]["archive"]["results"] is True and results_workspace_config ] if successful_work_to_transfer: transfer_status["successful_work_transferred"] = deposit_work_to_results( @@ -158,9 +166,12 @@ def transfer(test_flag: bool, buckets: Buckets, results: Results) -> Dict[str, A work for work in failed_work if work["config"]["archive"]["results"] is False + and not results_workspace_config ] failed_work_to_transfer = [ - work for work in failed_work if work["config"]["archive"]["results"] is True + work + for work in failed_work + if work["config"]["archive"]["results"] is True and results_workspace_config ] if failed_work_to_transfer: diff --git a/workflow/definitions/config.py b/workflow/definitions/config.py index b29881c..aa9593a 100644 --- a/workflow/definitions/config.py +++ b/workflow/definitions/config.py @@ -65,7 +65,7 @@ def validate_archive(cls, value: str) -> str: Returns: str: The archive strategy. """ - strategy = ["pass", "copy", "move", "delete", "upload"] + strategy = ["bypass", "copy", "delete", "move"] if value not in strategy: raise ValueError(f"archive strategy must be one of {strategy}") return value diff --git a/workflow/lifecycle/archive.py b/workflow/lifecycle/archive.py deleted file mode 100644 index 721b849..0000000 --- a/workflow/lifecycle/archive.py +++ /dev/null @@ -1,156 +0,0 @@ -"""Archive lifecycle module.""" -import os -import shutil -import subprocess -from datetime import datetime -from pathlib import Path -from typing import Any, Dict, List, Optional - -from workflow.definitions.work import Work -from workflow.utils.logger import get_logger - -logger = get_logger("workflow") - - -def copy(path: Path, payload: Optional[List[str]]) -> bool: - """Copy the work products to the archive. - - Args: - path (Path): Destination path. - payload (List[str]): List of files to copy. - """ - try: - path.mkdir(parents=True, exist_ok=True) - if not path.exists() or not path.is_dir() or not os.access(path, os.W_OK): - logger.error("Destination path is invalid or not writable.") - return False - if not payload: - logger.info("No files in payload.") - return True - for index, item in enumerate(payload): - if not os.path.exists(item): - logger.warning(f"File {item} does not exist.") - continue - shutil.copy(item, path.as_posix()) - payload[index] = (path / item.split("/")[-1]).as_posix() - return True - except Exception as error: - logger.exception(error) - return False - - -def move(path: Path, payload: Optional[List[str]]) -> bool: - """Move the work products to the archive. - - Args: - path (Path): Destination path. - payload (List[str]): List of products to move. - """ - status: bool = False - try: - path.mkdir(parents=True, exist_ok=True) - if path.exists() and path.is_dir() and os.access(path, os.W_OK) and payload: - for index, item in enumerate(payload): - shutil.move(item, path.as_posix()) - payload[index] = (path / item.split("/")[-1]).as_posix() - elif not payload: - logger.info("No files in payload.") - status = True - except Exception as error: - logger.exception(error) - status = False - finally: - return status - - -def delete(path: Path, payload: None | List[str]) -> bool: - """Delete the work products from the archive. - - Args: - path (Path): Destination path. - payload (List[str]): List of products to delete. - """ - status: bool = False - try: - if payload: - for item in payload: - os.remove(item) - payload.remove(item) - else: - logger.info("no files to delete.") - status = True - except Exception as error: - logger.exception(error) - finally: - return status - - -def upload(path: Path, payload: Optional[List[str]]) -> bool: - """Upload the work products to the archive. - - Args: - path (Path): Destination path. - payload (List[str]): List of products to upload. - - Returns: - bool: True if the upload was successful, False otherwise. - """ - logger.warning("upload currently not implemented") - raise NotImplementedError - - -def permissions(path: Path, site: str) -> bool: - """Set the permissions for the work products in the archive.""" - status: bool = False - try: - if site == "canfar": - subprocess.run(f"setfacl -R -m g:chime-frb-ro:r {path.as_posix()}") - subprocess.run(f"setfacl -R -m g:chime-frb-rw:rw {path.as_posix()}") - status = True - except FileNotFoundError as error: - logger.warning(error) - logger.debug( - "Linux tool 'acl' not installed, trying chgrp and chmod instead." # noqa: E501 - ) - try: - subprocess.run(f"chgrp -R chime-frb-rw {path.as_posix()}") - subprocess.run(f"chmod g+w {path.as_posix()}") - status = True - except Exception as error: - logger.warning(error) - status = False - finally: - return status - - -def run(work: Work, workspace: Dict[str, Any]): - """Run the archive lifecycle for a work object. - - Args: - work (Work): The work object to run the archive lifecycle for. - workspace (Dict[str, Any]): The workspace configuration. - """ - try: - # workspace: Dict[str, Any] = read.workspace(DEFAULT_WORKSPACE_PATH.as_posix()) - mounts: Dict[str, Any] = workspace.get("archive", {}).get("mounts", {}) - changes: bool = False - actions = { - "copy": copy, - "move": move, - "delete": delete, - "upload": upload, - } - date = datetime.fromtimestamp(work.creation).strftime("%Y%m%d") # type: ignore - path: Path = Path( - f"{mounts.get(work.site)}/workflow/{date}/{work.pipeline}/{work.id}" - ) - if work.config.archive.products != "pass" and work.products: - actions[work.config.archive.products](path, work.products) - changes = True - if work.config.archive.plots != "pass" and work.plots: - actions[work.config.archive.plots](path, work.plots) - changes = True - if changes: - permissions(path, work.site) - except Exception as error: - logger.warning(error) diff --git a/workflow/lifecycle/archive/__init__.py b/workflow/lifecycle/archive/__init__.py new file mode 100644 index 0000000..8ad1264 --- /dev/null +++ b/workflow/lifecycle/archive/__init__.py @@ -0,0 +1,100 @@ +"""Archive lifecycle module.""" +from datetime import datetime +from pathlib import Path +from typing import Any, Dict + +from workflow.definitions.work import Work +from workflow.lifecycle.archive import http, posix, s3 +from workflow.utils import logger + +log = logger.get_logger("workflow.lifecycle.archive") + + +def run(work: Work, workspace: Dict[str, Any]) -> None: + """Run the archive lifecycle for a work object. + + Args: + work (Work): The work object to run the archive lifecycle for. + workspace (Dict[str, Any]): The workspace configuration. + """ + try: + mounts: Dict[str, Any] = workspace.get("archive", {}).get("mounts", {}) + archive_config: Dict[str, Any] = workspace.get("config", {}).get("archive", {}) + changes: bool = False + actions = { + "s3": { + "bypass": s3.bypass, + "copy": s3.copy, + "delete": s3.delete, + "move": s3.move, + }, + "posix": { + "bypass": posix.bypass, + "copy": posix.copy, + "delete": posix.delete, + "move": posix.move, + }, + "http": { + "bypass": http.bypass, + "copy": http.copy, + "delete": http.delete, + "move": http.move, + }, + } + if work.creation: + date: str = datetime.fromtimestamp(work.creation).strftime("%Y%m%d") + path: Path = Path( + f"{mounts.get(work.site)}/workflow/{date}/{work.pipeline}/{work.id}" + ) + + if ( + work.config.archive.products + in archive_config.get("products", {}).get("methods", []) + and work.products + ): + storage: str = archive_config.get("products", {}).get("storage", "") + if storage in actions.keys(): + actions[storage][work.config.archive.products]( + path, + work.products, + ) + changes = True + else: + log.warning( + f"Archive storage {storage} not supported, or storage has not been set for products in workspace." # noqa: E501 + ) + elif work.config.archive.products not in archive_config.get("products", {}).get( + "methods", [] + ): + log.warning( + f"Archive method {work.config.archive.products} not allowed for products by workspace." # noqa: E501 + ) + + if ( + work.config.archive.plots + in archive_config.get("plots", {}).get("methods", []) + and work.plots + ): + storage = archive_config.get("plots", {}).get("storage", "") + if storage in actions.keys(): + actions[storage][work.config.archive.plots]( + path, + work.plots, + ) + changes = True + else: + log.warning( + f"Archive storage {storage} not supported, or storage has not been set for plots in workspace." # noqa: E501 + ) + elif work.config.archive.plots not in archive_config.get("plots", {}).get( + "methods", [] + ): + log.warning( + f"Archive method {work.config.archive.plots} not allowed for plots by workspace." # noqa: E501 + ) + if changes and "posix" in archive_config.get("permissions", {}): + posix.permissions( + path, archive_config.get("permissions", {}).get("posix", {}) + ) + except Exception as error: + log.warning(error) diff --git a/workflow/lifecycle/archive/http.py b/workflow/lifecycle/archive/http.py new file mode 100644 index 0000000..66f8f94 --- /dev/null +++ b/workflow/lifecycle/archive/http.py @@ -0,0 +1,57 @@ +"""HTTP archive functions.""" +from pathlib import Path +from typing import List, Optional + +from workflow.utils import logger + +log = logger.get_logger("workflow.lifecycle.archive.http") + + +def bypass(path: Path, payload: Optional[List[str]]) -> bool: + """Bypass the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of files to copy. + """ + log.info("Bypassing archive.") + return True + + +def copy(path: Path, payload: Optional[List[str]]) -> bool: + """Copy the work products to the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of files to copy. + """ + log.warning("upload currently not implemented") + raise NotImplementedError + + +def move(path: Path, payload: Optional[List[str]]) -> bool: + """Move the work products to the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of products to move. + """ + log.warning("upload currently not implemented") + raise NotImplementedError + + +def delete(path: Path, payload: None | List[str]) -> bool: + """Delete the work products from the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of products to delete. + """ + log.warning("delete currently not implemented") + raise NotImplementedError + + +def permissions(path: Path, site: str) -> bool: + """Set the permissions for the work products in the archive.""" + log.warning("permissions currently not implemented") + raise NotImplementedError diff --git a/workflow/lifecycle/archive/posix.py b/workflow/lifecycle/archive/posix.py new file mode 100644 index 0000000..4c96ce9 --- /dev/null +++ b/workflow/lifecycle/archive/posix.py @@ -0,0 +1,136 @@ +"""POSIX archive functions.""" +import os +import shutil +import subprocess +from pathlib import Path +from typing import Any, Dict, List, Optional + +from workflow.utils import logger + +log = logger.get_logger("workflow.lifecycle.archive.posix") + + +def bypass(path: Path, payload: Optional[List[str]]) -> bool: + """Bypass the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of files to copy. + """ + log.info("Bypassing archive.") + return True + + +def copy(path: Path, payload: Optional[List[str]]) -> bool: + """Copy the work products to the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of files to copy. + """ + try: + path.mkdir(parents=True, exist_ok=True) + if not path.exists() or not path.is_dir() or not os.access(path, os.W_OK): + log.error("Destination path is invalid or not writable.") + return False + if not payload: + log.info("No files in payload.") + return True + for index, item in enumerate(payload): + if not os.path.exists(item): + log.warning(f"File {item} does not exist.") + continue + shutil.copy(item, path.as_posix()) + payload[index] = (path / item.split("/")[-1]).as_posix() + return True + except Exception as error: + log.exception(error) + return False + + +def move(path: Path, payload: Optional[List[str]]) -> bool: + """Move the work products to the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of products to move. + """ + status: bool = False + try: + path.mkdir(parents=True, exist_ok=True) + if path.exists() and path.is_dir() and os.access(path, os.W_OK) and payload: + for index, item in enumerate(payload): + shutil.move(item, path.as_posix()) + payload[index] = (path / item.split("/")[-1]).as_posix() + elif not payload: + log.info("No files in payload.") + status = True + except Exception as error: + log.exception(error) + status = False + finally: + return status + + +def delete(path: Path, payload: None | List[str]) -> bool: + """Delete the work products from the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of products to delete. + """ + status: bool = False + try: + if payload: + for item in payload: + os.remove(item) + payload.remove(item) + else: + log.info("no files to delete.") + status = True + except Exception as error: + log.exception(error) + finally: + return status + + +def permissions(path: Path, config: Dict[str, Any]) -> bool: + """Set the permissions for the work products in the archive.""" + status: bool = False + try: + if not path.exists(): + raise NotADirectoryError + + user: str | None = config.get("user") + group: str | None = config.get("group") + if not user and not group: + raise ValueError("Either user or group must be specified.") + + command: str = config.get( + "command", + "chgrop -R {group} {path}; chmod -R g+w {path}", + ) + command = eval(f"f'{command}'") + subprocess.run(command) + status = True + + except NotADirectoryError: + log.error(f"Path {path.as_posix()} does not exist.") + status = False + + except ValueError as error: + log.error(error) + status = False + + except FileNotFoundError as error: + log.warning(error) + try: + subprocess.run(f"chgrp -R chime-frb-rw {path.as_posix()}") + subprocess.run(f"chmod g+w {path.as_posix()}") + status = True + except Exception as error: + log.warning(error) + status = False + + finally: + return status diff --git a/workflow/lifecycle/archive/s3.py b/workflow/lifecycle/archive/s3.py new file mode 100644 index 0000000..f3d7753 --- /dev/null +++ b/workflow/lifecycle/archive/s3.py @@ -0,0 +1,156 @@ +"""S3 archive functions.""" +import os +from pathlib import Path +from typing import List, Optional + +from minio import Minio + +from workflow.utils import logger + +log = logger.get_logger("workflow.lifecycle.archive.s3") + +WORKFLOW_S3_ENDPOINT = os.getenv("WORKFLOW_S3_ENDPOINT") +WORKFLOW_S3_ACCESS_KEY = os.getenv("WORKFLOW_S3_ACCESS_KEY") +WORKFLOW_S3_SECRET_KEY = os.getenv("WORKFLOW_S3_SECRET_KEY") +WORKFLOW_S3_BUCKET = os.getenv("WORKFLOW_S3_BUCKET", "workflow") + + +def bypass(path: Path, payload: Optional[List[str]]) -> bool: + """Bypass the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of files to copy. + """ + log.info("Bypassing archive.") + return True + + +def copy(path: Path, payload: Optional[List[str]]) -> bool: + """Copy the work products to the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of files to copy. + """ + try: + # Initialise minio client + log.info("Connecting to S3 storage to copy files") + log.debug(f"Endpoint: {WORKFLOW_S3_ENDPOINT}") + log.debug(f"Access Key: {WORKFLOW_S3_ACCESS_KEY}") + log.debug(f"Secret Key: {WORKFLOW_S3_SECRET_KEY}") + client = Minio( + endpoint=WORKFLOW_S3_ENDPOINT, + access_key=WORKFLOW_S3_ACCESS_KEY, + secret_key=WORKFLOW_S3_SECRET_KEY, + ) + log.info("Connected ✅") + # Check bucket exists and if not, create it + if not client.bucket_exists(WORKFLOW_S3_BUCKET): + log.info(f"Bucket {WORKFLOW_S3_BUCKET} does not exist. Creating it.") + client.make_bucket(WORKFLOW_S3_BUCKET) + # Check there are files to copy + if not payload: + log.info("No files in payload.") + return True + split_path = path.as_posix().split("/") + object_paths = "/".join(split_path[split_path.index("workflow") + 1 :]) + for index, item in enumerate(payload): + # Check file exists + if not os.path.exists(item): + log.warning(f"File {item} does not exist.") + continue + # Upload file to S3 + client.fput_object( + bucket_name=WORKFLOW_S3_BUCKET, + object_name="/".join([object_paths, item.split("/")[-1]]), + file_path=item, + ) + # Update payload with new path + payload[ + index + ] = f"s3://{os.getenv('WORKFLOW_S3_ENDPOINT')}/workflow/{'/'.join([object_paths, item.split('/')[-1]])}" # noqa: E501 + log.info("Move complete ✅") + return True + except Exception as error: + log.error("Move failed ❌") + log.exception(error) + return False + + +def move(path: Path, payload: Optional[List[str]]) -> bool: + """Move the work products to the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of products to move. + """ + try: + # Initialise minio client + log.info("Connecting to S3 storage to move files") + log.debug(f"Endpoint: {WORKFLOW_S3_ENDPOINT}") + log.debug(f"Access Key: {WORKFLOW_S3_ACCESS_KEY}") + log.debug(f"Secret Key: {WORKFLOW_S3_SECRET_KEY}") + client = Minio( + endpoint=WORKFLOW_S3_ENDPOINT, + access_key=WORKFLOW_S3_ACCESS_KEY, + secret_key=WORKFLOW_S3_SECRET_KEY, + ) + log.info("Connected ✅") + # Check bucket exists and if not, create it + if not client.bucket_exists(WORKFLOW_S3_BUCKET): + log.info(f"Bucket {WORKFLOW_S3_BUCKET} does not exist. Creating it.") + client.make_bucket(WORKFLOW_S3_BUCKET) + # Check there are files to copy + if not payload: + log.info("No files in payload.") + return True + split_path = path.as_posix().split("/") + object_paths = "/".join(split_path[split_path.index("workflow") + 1 :]) + for index, item in enumerate(payload): + # Check file exists + if not os.path.exists(item): + log.warning(f"File {item} does not exist.") + continue + # Upload file to S3 + client.fput_object( + bucket_name=WORKFLOW_S3_BUCKET, + object_name="/".join([object_paths, item.split("/")[-1]]), + file_path=item, + ) + # Update payload with new path + payload[ + index + ] = f"s3://{os.getenv('WORKFLOW_S3_ENDPOINT')}/workflow/{'/'.join([object_paths, item.split('/')[-1]])}" # noqa: E501 + # Delete file + os.remove(item) + log.info("Move complete ✅") + return True + except Exception as error: + log.error("Move failed ❌") + log.exception(error) + return False + + +def delete(path: Path, payload: None | List[str]) -> bool: + """Delete the work products from the archive. + + Args: + path (Path): Destination path. + payload (List[str]): List of products to delete. + """ + # TODO: Implement delete for S3 + # NOTE: Do we need a specific delete function for S3? + # Since Workflow always runs on a POSIX system, we can + # just use the POSIX delete function. + log.warning("delete currently not implemented") + raise NotImplementedError + + +def permissions(path: Path, site: str) -> bool: + """Set the permissions for the work products in the archive.""" + # TODO: Implement permissions for S3 + # NOTE: Permissions seems to be set on the bucket level, not the object level + # So, perhaps add this to a bucket creation function? + log.warning("permissions currently not implemented") + raise NotImplementedError diff --git a/workflow/utils/logger.py b/workflow/utils/logger.py index 372d22d..01f583e 100644 --- a/workflow/utils/logger.py +++ b/workflow/utils/logger.py @@ -2,9 +2,11 @@ import logging from datetime import datetime -from typing import Optional +from typing import Any, Dict, Optional import click +import requests +from logging_loki import LokiHandler from rich.logging import RichHandler @@ -49,6 +51,47 @@ def get_logger(name: Optional[str] = None, level: int = logging.INFO) -> logging return log +def add_loki_handler( + logger: logging.Logger, loki_url: str, workspace: Dict[str, Any] +) -> bool: + """Add a Loki handler to the logger. + + Args: + logger (Logger): Python logger + loki_url (str): Loki URL + + Raises: + AttributeError: Loki not ready. + + Returns: + bool: Loki handler status + """ + status: bool = False + try: + loki_sc = requests.get( + loki_url.replace("loki/api/v1/push", "ready") + ).status_code + if loki_sc == 200: + loki_handler = LokiHandler( + url=loki_url, + tags=workspace.get("config", {}).get("logging", {}).get("loki", {}), + version="1", + ) + loki_handler.setFormatter( + logging.Formatter("%(levelname)s %(tag)s %(name)s %(message)s") + ) + loki_handler.setLevel("ERROR") + logger.root.addHandler(loki_handler) + logger.debug(f"Loki URL: {loki_url}") + status = True + else: + raise AttributeError("Loki not ready.") + except Exception as error: + logger.debug(error) + finally: + return status + + class TagFilter(logging.Filter): """Filter log messages by tag.""" diff --git a/workflow/workspaces/chimefrb.yml b/workflow/workspaces/chimefrb.yml index 58c4096..fb52881 100644 --- a/workflow/workspaces/chimefrb.yml +++ b/workflow/workspaces/chimefrb.yml @@ -30,3 +30,18 @@ archive: s3: minion: url: "https://s3.us-west-2.amazonaws.com/frb-archiver" + +config: + archive: + results: true + plots: + methods: ["move", "delete"] # Defines the methods enabled by the workspace admin + storage: "s3" + permissions: List[Linux Groups]? + products: + methods: ["move", "delete"] # Can also be copy or delete + storage: "posix" + logging: + loki: + site: "local" + pipeline: "temp" diff --git a/workflow/workspaces/development.yml b/workflow/workspaces/development.yml index 8c523f3..5e9585c 100644 --- a/workflow/workspaces/development.yml +++ b/workflow/workspaces/development.yml @@ -26,7 +26,12 @@ http: config: archive: - results: "move" # Can also be copy or delete - plots: "move" # Can also be copy or delete - products: "move" # Can also be copy or delete + results: true + plots: + methods: ["move", "delete"] # Defines the methods enabled by the workspace admin + storage: "s3" + permissions: List[Linux Groups]? + products: + methods: ["move", "delete"] # Can also be copy or delete + storage: "posix" slack: diff --git a/workflow/workspaces/sample-test.yaml b/workflow/workspaces/sample-test.yaml new file mode 100644 index 0000000..5213eb4 --- /dev/null +++ b/workflow/workspaces/sample-test.yaml @@ -0,0 +1,40 @@ +workspace: testing + +sites: + - local + +archive: + mounts: + local: "/" + +config: + archive: + plots: + methods: + - "bypass" + - "copy" + - "delete" + - "move" + storage: "s3" + products: + methods: + - "bypass" + - "copy" + - "delete" + - "move" + storage: "posix" + results: true + permissions: + posix: + user: "user" + group: "chime-frb-ro" + command: "setfacl -R -m g:{group}:r {path}" + + http: + baseurls: + buckets: "http://localhost:8001" + loki: "http://localhost:8005/loki/api/v1/push" + minio: "http://localhost:8005" + pipelines: "http://localhost:8003" + products: "http://localhost:8004" + results: "http://localhost:8002"