diff --git a/.env.demo.bodc b/.env.demo.bodc index 6c0dcda..059bf1e 100644 --- a/.env.demo.bodc +++ b/.env.demo.bodc @@ -4,7 +4,6 @@ FILECHECKER_IMAGE_TAG=develop #availables tags at https://github.com/OneArgo/ArgoFormatChecker/tags + develop + latest # External directories to mount to the container -FILECHECKER_SPEC_VOLUME=./file_checker_spec FILECHECKER_INPUT_VOLUME=./demo/inputs/3901945 FILECHECKER_OUTPUT_VOLUME=./demo/outputs/3901945 diff --git a/.env.demo.coriolis b/.env.demo.coriolis index 02c5783..4ea5980 100644 --- a/.env.demo.coriolis +++ b/.env.demo.coriolis @@ -4,7 +4,6 @@ FILECHECKER_IMAGE_TAG=develop #availables tags at https://github.com/OneArgo/ArgoFormatChecker/tags + develop + latest # External directories to mount to the container -FILECHECKER_SPEC_VOLUME=./file_checker_spec FILECHECKER_INPUT_VOLUME=./demo/inputs/2903996 FILECHECKER_OUTPUT_VOLUME=./demo/outputs/2903996 diff --git a/.env.docs b/.env.docs index 1c793b6..b660a54 100644 --- a/.env.docs +++ b/.env.docs @@ -4,7 +4,6 @@ FILECHECKER_IMAGE_TAG=develop #availables tags at https://github.com/OneArgo/ArgoFormatChecker/tags + develop + latest # External directories to mount to the container -FILECHECKER_SPEC_VOLUME= FILECHECKER_INPUT_VOLUME= FILECHECKER_OUTPUT_VOLUME= diff --git a/.github/workflows/component-container-image.yml b/.github/workflows/component-container-image.yml index 68b5542..df4ab07 100644 --- a/.github/workflows/component-container-image.yml +++ b/.github/workflows/component-container-image.yml @@ -11,6 +11,14 @@ on: description: "Path of the docker image Tag" default: "ghcr.io/${{ github.repository }}/app" type: string + target: + description: "Target build stage for Docker multistage build" + required: false + type: string + file: + description: "Path to the Dockerfile." + required: false + type: string jobs: container-image-build: @@ -35,11 +43,20 @@ jobs: password: ${{ secrets.GITHUB_TOKEN }} - name: Build (pull request) uses: docker/build-push-action@v6 - if: ${{ github.event_name == 'pull_request'}} + if: ${{ github.event_name == 'pull_request' && (inputs.target == '' || inputs.target == null) }} with: context: "{{defaultContext}}:${{ inputs.context }}" tags: "${{ steps.format.outputs.lowercase }}:develop" push: false + - name: Build with target (pull request) + uses: docker/build-push-action@v6 + if: ${{ github.event_name == 'pull_request' && inputs.target != '' && inputs.target != null }} + with: + context: "{{defaultContext}}:${{ inputs.context }}" + target: ${{ inputs.target }} + file: ${{ inputs.file }} + tags: "${{ steps.format.outputs.lowercase }}:develop" + push: false - name: Build and push (develop) uses: docker/build-push-action@v6 if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/develop' }} @@ -49,15 +66,33 @@ jobs: push: true - name: Build and push (main) uses: docker/build-push-action@v6 - if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} + if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && (inputs.target == '' || inputs.target == null) }} with: context: "{{defaultContext}}:${{ inputs.context }}" tags: "${{ steps.format.outputs.lowercase }}:latest" push: true + - name: Build and push with target (main) + uses: docker/build-push-action@v6 + if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && inputs.target != '' && inputs.target != null }} + with: + context: "{{defaultContext}}:${{ inputs.context }}" + target: ${{ inputs.target }} + file: ${{ inputs.file }} + tags: "${{ steps.format.outputs.lowercase }}:latest" + push: true - name: Build and push (release) uses: docker/build-push-action@v6 - if: ${{ github.event_name == 'release' }} + if: ${{ github.event_name == 'release' && (inputs.target == '' || inputs.target == null) }} + with: + context: "{{defaultContext}}:${{ inputs.context }}" + tags: "${{ steps.format.outputs.lowercase }}:${{ github.ref_name }}" + push: true + - name: Build and push with target (release) + uses: docker/build-push-action@v6 + if: ${{ github.event_name == 'release' && inputs.target != '' && inputs.target != null }} with: context: "{{defaultContext}}:${{ inputs.context }}" + target: ${{ inputs.target }} + file: ${{ inputs.file }} tags: "${{ steps.format.outputs.lowercase }}:${{ github.ref_name }}" push: true diff --git a/.github/workflows/workflow-java.yml b/.github/workflows/workflow-java.yml index fbf77df..0370738 100644 --- a/.github/workflows/workflow-java.yml +++ b/.github/workflows/workflow-java.yml @@ -8,10 +8,14 @@ on: - develop paths: - file_checker_exec/** + - file_checker_spec/** + - Dockerfile pull_request: # Run for any pull requests paths: - file_checker_exec/** + - file_checker_spec/** + - Dockerfile release: types: [created] @@ -20,5 +24,5 @@ jobs: container-image-build: uses: ./.github/workflows/component-container-image.yml with: - context: file_checker_exec + context: . image-path: ghcr.io/OneArgo/ArgoFormatChecker/app \ No newline at end of file diff --git a/.github/workflows/workflow-python.yml b/.github/workflows/workflow-python.yml new file mode 100644 index 0000000..78dbe18 --- /dev/null +++ b/.github/workflows/workflow-python.yml @@ -0,0 +1,33 @@ +name: Image build + +on: + push: + branches: + # Run on our main branch + - main + - develop + paths: + - file_checker_python/** + pull_request: + # Run for any pull requests + paths: + - file_checker_python/** + release: + types: [created] + + +jobs: + container-image-build-wrapper: + uses: ./.github/workflows/component-container-image.yml + with: + context: . + file: "python.Dockerfile" + target: file-checker-python + image-path: ghcr.io/OneArgo/ArgoFormatChecker/python-wrapper + container-image-build-api: + uses: ./.github/workflows/component-container-image.yml + with: + context: . + file: "python.Dockerfile" + target: file-checker-api + image-path: ghcr.io/OneArgo/ArgoFormatChecker/python-api \ No newline at end of file diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b775174..5357970 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -2,8 +2,6 @@ include: - component: $CI_SERVER_FQDN/dev-ops/templates/automatisation/ci-cd/pipeline-java-container-image@~latest inputs: - container_image_build_context: "./file_checker_exec" - container_image_docker_file_path: "./file_checker_exec/Dockerfile" java_builder_artifacts_path: "**/target/*.{war,jar}" java_builder_build_command: "clean package -f file_checker_exec/pom.xml" java_builder_maven_quality_enable: "false" diff --git a/file_checker_exec/Dockerfile b/Dockerfile similarity index 85% rename from file_checker_exec/Dockerfile rename to Dockerfile index c459e60..ba2b19f 100644 --- a/file_checker_exec/Dockerfile +++ b/Dockerfile @@ -11,10 +11,11 @@ LABEL org.opencontainers.image.vendor="OneArgo" WORKDIR /build -COPY ./.mvn ./.mvn -COPY ./mvnw ./mvnw -COPY ./pom.xml ./pom.xml -COPY ./src ./src +COPY ./file_checker_exec/.mvn ./.mvn +COPY ./file_checker_exec/mvnw ./mvnw +COPY ./file_checker_exec/pom.xml ./pom.xml +COPY ./file_checker_exec/src ./src + # Ensure mvnw has execution permissions RUN chmod +x ./mvnw \ @@ -36,6 +37,9 @@ RUN set -e \ # Copy the built jar file to the runtime stage COPY --from=builder --chown=root:gcontainer --chmod=750 /build/target/file_checker*.jar app.jar +# Copy the specs : +COPY file_checker_spec /app/file_checker_spec + # Specify the default command for running the app ENTRYPOINT ["java", "-jar", "/app/app.jar"] diff --git a/README.md b/README.md index 0403056..fe7d339 100644 --- a/README.md +++ b/README.md @@ -28,13 +28,19 @@ $FILES_NAMES is a list of file's name from the INPUT_DIR. It is optional : witho ### Run the application using Docker +```bash +docker run --rm -v [ABSOLUTE_PATH_TO_DATA_FOLDER]:/app/data -v [ABSOLUTE_PATH_TO_OUTPUT_DIR]:/app/results ghcr.io/oneargo/argoformatchecker/app:{TAG} [$OPTIONS] $DAC_NAME ./file_checker_spec ./results ./data [$FILES_NAMES] +``` + +Or if you want to use your own specification files : + ```bash docker run --rm -v [ABSOLUTE_PATH_TO_SPEC]:/app/file_checker_spec -v [ABSOLUTE_PATH_TO_DATA_FOLDER]:/app/data -v [ABSOLUTE_PATH_TO_OUTPUT_DIR]:/app/results ghcr.io/oneargo/argoformatchecker/app:{TAG} [$OPTIONS] $DAC_NAME ./file_checker_spec ./results ./data [$FILES_NAMES] ``` You need to mount external directories to the container : -[ABSOLUTE_PATH_TO_SPEC] : the file_checker_spec directory path. +[ABSOLUTE_PATH_TO_SPEC] : OPTIONAL - The file_checker_spec directory path (if you don't want to use the specs included in the docker container). [ABSOLUTE_PATH_TO_DATA_FOLDER] : Path to directory containing the argo necdf files to be checked. The fileChecker will not seek files in subfolders @@ -43,7 +49,7 @@ You need to mount external directories to the container : Example : ```bash -docker run --rm -v D:\test_file_checker\file_checker_spec:/app/file_checker_spec -v D:\test_file_checker\datatest:/app/data -v D:\test_file_checker\results:/app/results ghcr.io/oneargo/argoformatchecker/app:develop -no-name-check coriolis ./file_checker_spec ./results ./data +docker run --rm -v D:\test_file_checker\datatest:/app/data -v D:\test_file_checker\results:/app/results ghcr.io/oneargo/argoformatchecker/app:develop -no-name-check coriolis ./file_checker_spec ./results ./data ``` ### Run the application using Docker Compose @@ -73,7 +79,6 @@ FILECHECKER_IMAGE=ghcr.io/oneargo/argoformatchecker/app FILECHECKER_IMAGE_TAG=develop # External directories to mount to the container -FILECHECKER_SPEC_VOLUME='D:\test_compose\file_checker_spec' FILECHECKER_INPUT_VOLUME='D:\test_compose\data' FILECHECKER_OUTPUT_VOLUME='D:\test_compose\results' @@ -107,12 +112,20 @@ or for Windows : output files will be generated in `./demo/outputs`. +### Run File checker using Python and an API + +In folder /file-checker-python you will find a python wrapper and an API to facilitate the use of Argo FileChecker. See python.README for more informations. + ### Test data To further test the Argo File Checker, you will find argo data here : https://www.argodatamgt.org/DataAccess.html The Argo File Checker is not yet designed to checking *prof.nc and *Sprof.nc. It checks only TRAJ, META, TECH and PROFILES files. +## Run File checker using Python and an API + +In folder /argo-file-checker-python you will find a python wrapper and an API to facilitate the use of Argo FileChecker. + ## TOOLS ### Maven Wrapper diff --git a/compose.yaml b/compose.yaml index 4a71e93..1d03d2c 100644 --- a/compose.yaml +++ b/compose.yaml @@ -5,8 +5,7 @@ services: user: "${DOCKER_UID:-0}:${DOCKER_GID:-0}" group_add: - 1001 - volumes: - - ${FILECHECKER_SPEC_VOLUME}:/app/file_checker_spec:ro + volumes: - ${FILECHECKER_INPUT_VOLUME}:/app/data:ro - ${FILECHECKER_OUTPUT_VOLUME}:/app/results:rw command: ${FILECHECKER_OPTIONS} ${DAC_NAME} ./file_checker_spec ./results ./data ${FILES_NAMES} \ No newline at end of file diff --git a/file_checker_exec/dockerignore b/dockerignore similarity index 100% rename from file_checker_exec/dockerignore rename to dockerignore diff --git a/file_checker_exec/pom.xml b/file_checker_exec/pom.xml index 7e8a97f..8cab763 100644 --- a/file_checker_exec/pom.xml +++ b/file_checker_exec/pom.xml @@ -4,7 +4,7 @@ 4.0.0 fr.ifremer file_checker_exec - 2.9.3 + 2.9.4 Argo NetCDF file format checker diff --git a/file_checker_exec/src/main/java/fr/coriolis/checker/validators/ArgoFileValidator.java b/file_checker_exec/src/main/java/fr/coriolis/checker/validators/ArgoFileValidator.java index 9c5a457..5b67c9b 100644 --- a/file_checker_exec/src/main/java/fr/coriolis/checker/validators/ArgoFileValidator.java +++ b/file_checker_exec/src/main/java/fr/coriolis/checker/validators/ArgoFileValidator.java @@ -514,10 +514,12 @@ private boolean checkSpecialTechParamVarAttributeValue(Variable dataVar, String if (attrName.equals("long_name") && authorizedLongName != null && !authorizedLongName.contains(dataAttrValue)) { - validationResult.addError("attribute: " + varName + ":" + attrName + ": Definitions differ " - + "\n\tSpecification = See argo-tech_names-spec list, definition column" - + "\n\tData File = '" + dataAttrValue + "'"); + String specValueInErrorReport = authorizedLongName.size() == 1 ? "'" + authorizedLongName.get(0) + "'" + : "Multiple possibilities; see argo-tech_names-spec list, definition column"; + validationResult.addError( + String.format("attribute: %s:%s: Definitions differ\n\tSpecification = %s\n\tData File = '%s'", + varName, attrName, specValueInErrorReport, dataAttrValue)); } } diff --git a/file_checker_python/file_checker_python_api/README.md b/file_checker_python/file_checker_python_api/README.md new file mode 100644 index 0000000..e69de29 diff --git a/file_checker_python/file_checker_python_api/file_checker_api/__init__.py b/file_checker_python/file_checker_python_api/file_checker_api/__init__.py new file mode 100644 index 0000000..c07c459 --- /dev/null +++ b/file_checker_python/file_checker_python_api/file_checker_api/__init__.py @@ -0,0 +1 @@ +from .app import app diff --git a/file_checker_python/file_checker_python_api/file_checker_api/app.py b/file_checker_python/file_checker_python_api/file_checker_api/app.py new file mode 100644 index 0000000..eac44a0 --- /dev/null +++ b/file_checker_python/file_checker_python_api/file_checker_api/app.py @@ -0,0 +1,55 @@ +import os +import shutil +from fastapi import FastAPI, UploadFile +from pathlib import Path +from tempfile import TemporaryDirectory + +from argofilechecker_python_wrapper import FileChecker, ValidationResult + +ROOT_PATH = os.getenv("API_ROOT_PATH", "") +UPLOAD_FILES_DIR = Path(os.getenv("UPLOAD_FILES_DIR", Path.cwd())) + +app = FastAPI(root_path=ROOT_PATH) + + +@app.get("/") +def app_status() -> dict[str, str]: + """ + Health check endpoint to confirm that the app is running. + :return: status message + """ + return {"status": "OK"} + + +@app.post("/check-files") +def check_file_list(files: list[UploadFile], dac: str) -> list[ValidationResult]: + """ + Main endpoint to upload files to be checked. + :param files: + List of files uploaded as multipart/form-data + :param dac: + Relevant DAC for the files, e.g. coriolis, bodc, aoml, etc. Must be the same DAC for all files + + :return: + list[ValidationResult] + """ + if not files: + raise ValueError("No files to check.") + if not UPLOAD_FILES_DIR.exists(): + raise FileNotFoundError(f"Upload directory does not exist: {UPLOAD_FILES_DIR}") + if not UPLOAD_FILES_DIR.is_dir(): + raise NotADirectoryError(f"Upload directory path is not a directory: {UPLOAD_FILES_DIR}") + + with TemporaryDirectory(dir=UPLOAD_FILES_DIR) as request_tmp_dir: + request_file_dir = Path(request_tmp_dir) + for upload_file in files: + try: + with request_file_dir.joinpath(upload_file.filename).open("wb") as buffer: + shutil.copyfileobj(upload_file.file, buffer) + finally: + upload_file.file.close() + file_checker = FileChecker() + results = file_checker.check_files(request_file_dir.glob("*"), dac) + if not results: + raise RuntimeError("An error occurred while handling uploaded files.") + return results diff --git a/file_checker_python/file_checker_python_api/poetry.lock b/file_checker_python/file_checker_python_api/poetry.lock 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a/file_checker_python/file_checker_python_wrapper/.gitignore b/file_checker_python/file_checker_python_wrapper/.gitignore new file mode 100644 index 0000000..820ba55 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/.gitignore @@ -0,0 +1,26 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# Distribution / packaging +build/ +dist/ +public/ +*.egg-info/ +.eggs/ +docs/source/generated + +# Test artifacts= + +.coverage +coverage.xml +coverage_reports +junit.xml + +# Developer Environments +venv/ +.tox/ +./ruff_cache +./mypy_cache +.env +secrets.env diff --git a/file_checker_python/file_checker_python_wrapper/README.md b/file_checker_python/file_checker_python_wrapper/README.md new file mode 100644 index 0000000..e69de29 diff --git a/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_docker.py b/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_docker.py new file mode 100644 index 0000000..1af6701 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_docker.py @@ -0,0 +1,25 @@ +"""Demo script to use argofilechecker_python_wrapper in docker container.""" + +import os +from typing import List + +from argofilechecker_python_wrapper import FileChecker, ValidationResult +from argofilechecker_python_wrapper.models import ResultType + + +# 1) Instantiate the wrapper (explicit paths). +# file checker jar is already contained in the docker image +file_checker = FileChecker() + + +# 2) Validate a list of files from the same DAC +list_files = [f"/data/{file}" for file in os.listdir("/data")] +validation_results: List[ValidationResult] = file_checker.check_files(list_files, "coriolis") + +# 3) Iterate over the results +for file_result in validation_results: + print(file_result.to_string()) + + if file_result.result in {ResultType.FAILURE, ResultType.ERROR}: + print(*file_result.errors_messages) + print(*file_result.warnings_messages) diff --git a/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_test.py b/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_test.py new file mode 100644 index 0000000..06e62b4 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_test.py @@ -0,0 +1,26 @@ +"""Demo script to use argofilechecker_python_wrapper.""" + +import os +from typing import List + +from argofilechecker_python_wrapper import FileChecker, ValidationResult +from argofilechecker_python_wrapper.models import ResultType + +jar_path = "./file_checker_exec-2.9.3-SNAPSHOT.jar" +spec_path = "./file_checker_spec" + + +# 1) Instantiate the wrapper (explicit paths) +file_checker = FileChecker(jar_path, spec_path) + +# 2) Validate a list of files from the same DAC +list_files = [f"./test_data/2903996/{file}" for file in os.listdir("./test_data/2903996")] +validation_results: List[ValidationResult] = file_checker.check_files(list_files, "coriolis") + +# 3) Iterate over the 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"104514a4a31881642b004e6fef032ad7a79f3b6da539d42db88484f6ba6d14b2" diff --git a/file_checker_python/file_checker_python_wrapper/pyproject.toml b/file_checker_python/file_checker_python_wrapper/pyproject.toml new file mode 100644 index 0000000..82413cd --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/pyproject.toml @@ -0,0 +1,189 @@ +[build-system] +requires = ["poetry-core>=2.0.0,<3.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"] +build-backend = "poetry_dynamic_versioning.backend" + +[project] +name = "argofilechecker-python-wrapper" +version = "0.0.0" +description = "Python wrapper for Argo file checker" +authors = [ + {name = "Yvan Lubac",email = "yvan.lubac@euro-argo.eu"} +] +readme = "README.md" + +[tool.poetry] +packages = [{include = "argofilechecker_python_wrapper", from = "src"}] + +[tool.poetry-dynamic-versioning] +enable = true +vcs = "git" +style = "semver" + +[tool.poetry.dependencies] +python = ">=3.10,<4.0" +pydantic = "^2.11.9" +defusedxml = "^0.7.1" +# Specify the optional dependencies that will be used below as "extras" +pytest = { version = ">=8.4.2,<9.0.0", optional = true } +pytest-cov = { version = ">=7.0.0,<8.0.0", optional = true } +pytest-mock = { version = ">=3.15.1,<4.0.0", optional = true } +coverage = { version = ">=7.10.6,<8.0.0", extras = ["xml"], optional = true } +tox = { version = ">=4.30.2,<5.0.0", optional = true } +ruff = { version = ">=0.13.0,<0.14.0", optional = true } +mypy = { version = ">=1.18.1,<2.0.0", optional = true } +bandit = { version = ">=1.8.6,<2.0.0", extras = ["toml"], optional = true } +poetry = { version = ">=2.0.0", optional = true } +twine = { version = ">=6.2.0,<7.0.0", optional = true } +pytest-env = "^1.1.5" + + +[tool.poetry.extras] +test = ["pytest", "pytest-cov", "pytest-mock", "pytest-env", "coverage", "tox"] +lint = ["ruff"] +type = ["mypy"] +bandit = ["bandit"] +build = ["poetry", "twine"] + + +[dependency-groups] +lint = [ + "ruff (>=0.13.0,<0.14.0)" +] +build = [ + "twine (>=6.2.0,<7.0.0)" +] +type = [ + "mypy (>=1.18.1,<2.0.0)" +] +test = [ + "pytest (>=8.4.2,<9.0.0)", + "pytest-cov (>=7.0.0,<8.0.0)", + "pytest-mock (>=3.15.1,<4.0.0)", + "tox (>=4.30.2,<5.0.0)", + "coverage[xml] (>=7.10.6,<8.0.0)" +] +bandit = [ + "bandit[toml] (>=1.8.6,<2.0.0)" +] + +[tool.coverage.paths] +source = [ + "src/argofilechecker_python_wrapper", + "**/argofilechecker_python_wrapper" +] + +[tool.setuptools.packages.find] +namespaces = false + +[tool.bandit] +exclude_dirs = ["tests"] + +[tool.ruff] +target-version = "py312" +line-length = 120 +indent-width = 4 +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".git-rewrite", + ".hg", + ".ipynb_checkpoints", + ".mypy_cache", + ".nox", + ".pants.d", + ".pyenv", + ".pytest_cache", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + ".vscode", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "site-packages", + "venv", +] + +[tool.ruff.lint] +select = [ + "F", + "E", + "C90", + "I", + "N", + "D", + "ERA", + "PD", + "PGH", + "PL", + "TRY", + "FLY", + "NPY", + "PERF", + "FURB", + "RUF" +] +ignore = [ + "D203", # Conflict with D211 - prefer no-blank-line-before-class. + "D213", # Conflict with D213 - prefer multi-line-summary-first-line. +] +fixable = ["ALL"] +unfixable = [] +# Allow unused variables when underscore-prefixed. +dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" +isort.split-on-trailing-comma = false + +[tool.ruff.format] +quote-style = "double" +indent-style = "space" +skip-magic-trailing-comma = true +line-ending = "auto" +docstring-code-format = true +docstring-code-line-length = "dynamic" + +[tool.mypy] +python_version = "3.12" +plugins = ["pydantic.mypy"] +disallow_any_unimported = true +disallow_any_expr = true +disallow_any_decorated = true +disallow_any_generics = true +disallow_any_explicit = true +disallow_subclassing_any = true +disallow_untyped_calls = true +disallow_untyped_defs = true +disallow_incomplete_defs = true +check_untyped_defs = true +disallow_untyped_decorators = true +no_implicit_optional = true +warn_unused_ignores = true +warn_no_return = true +warn_return_any = true +warn_redundant_casts = true +strict_equality = true +warn_unused_configs = true +ignore_missing_imports = true + +[tool.pydantic-mypy] +init_forbid_extra = true +init_typed = true +warn_required_dynamic_aliases = true + +[tool.pytest.ini_options] +testpaths = ["tests"] +markers = [ + "e2e: end-to-end tests which have to download data from GDAC."] + +[tool.pytest_env] +GDAC_FTP_HOST="ftp://ftp.ifremer.fr/ifremer/argo/dac" +SPECS_REPO_URL="https://github.com/OneArgo/ArgoFormatChecker.git" +SPECS_REPO_REF="main" +TEST_REPO_SUBDIR="file_checker_spec/" +JAR_URL="https://github.com/OneArgo/ArgoFormatChecker/releases/download/v2.9.3/file_checker_exec-2.9.3.jar" diff --git a/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/__init__.py b/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/__init__.py new file mode 100644 index 0000000..bf75c97 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/__init__.py @@ -0,0 +1,9 @@ +"""File Checker Python wrapper package.""" + +__version__ = "0.0.0" # version will be updated automatically by poetry_dynamic_versioning + + +from .file_checker import FileChecker +from .models import PhaseType, ResultType, ValidationResult + +__all__ = ["FileChecker", "PhaseType", "ResultType", "ValidationResult", "__version__"] diff --git a/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/file_checker.py b/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/file_checker.py new file mode 100644 index 0000000..7b42649 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/file_checker.py @@ -0,0 +1,311 @@ +"""FileChecker python wrapper module.""" + +import logging +import os +import subprocess # nosec B404 +import tempfile +from pathlib import Path +from typing import Dict, List, Optional +from xml.etree.ElementTree import Element, ElementTree, ParseError # nosec B405: this import is just for type. + +import defusedxml.ElementTree as DefusedET + +from .models import PhaseType, ResultType, ValidationResult + +logger = logging.getLogger(__name__) + + +class FileChecker: + """Python Wrapper for Argo Netcdf File Checker. + + File Checker will is run as subprocess so the location of the JAR file and specs must be provided as ENV variables + or explicitly in init. + The env vars are used in dockerfile : + The jar is included in file checker Docker image. + The spec dir could be included in the image in a future version of File Checker. + + Example: + # Explicit paths + checker = FileChecker("D:/test_checker/file_checker_exec-2.9.3.jar", "D:/test_checker/file_checker_spec") + + # Using environment variables (Docker) + checker = FileChecker() # Uses env vars + + """ + + def __init__(self, jar_path: Optional[str] = None, specs_path: Optional[str] = None): + """Initialize the File Checker. + + Args: + jar_path : Path to the File Checker .jar file. + If None -> use the FILE_CHECKER_JAR env var. + specs_path : Path to the specification (file_checker_spec) directory. + If None -> use the FILE_CHECKER_SPECS env var. + + Raises: + FileNotFoundError: If JAR or spec path don't exist + ValueError: If paths not provided and env vars not set + + """ + jar_path = jar_path or os.getenv("FILE_CHECKER_JAR") + specs_path = specs_path or os.getenv("FILE_CHECKER_SPECS") + + # checks : + if jar_path is None: + logger.error("jar_path not provided and FILE_CHECKER_JAR environment variable not defined") + raise ValueError + else: + self.jar_path = Path(jar_path) + if specs_path is None: + logger.error("jar_path not provided and FILE_CHECKER_JAR environment variable not defined") + raise ValueError + else: + self.specs_path = Path(specs_path) + + if not self.jar_path.exists(): + logger.error(f"File checker .jar file not found: {self.jar_path}") + raise FileNotFoundError + if not self.specs_path.exists(): + logger.error(f"Spec directory not found at : {self.specs_path}") + raise FileNotFoundError + + def check_files(self, files_paths_str: List[str], dac_name: str, options: list[str] = []) -> List[ValidationResult]: + """Check a list of files from a same dac using the File Checker. + + Args : + file_paths (list[str]) : list of files to checks. + ex : ['D:/data/file1.nc', 'D:/data/file2.nc', 'D:/other_data/file3.nc'] + dac_name (str) : dac name of the files : coriolis, bodc, aoml, etc. Must be the same DAC for all files. + options (list[str]) : list of file checker options. ex: ['-no-name-check'] + + Return : a list of ValidationResult objects containing the file checker results for each input files + + """ + if not files_paths_str: + logger.error("file_paths list cannot be empty") + raise ValueError + + # check if all files exist : + existing_files, missing_files = self._get_valid_files_path(files_paths_str) + if len(missing_files) > 0: + warning_msg = f"{len(missing_files)} file(s) was/were not found" + logger.warning(warning_msg) + if len(existing_files) == 0: + logger.error("No existing files were found") + raise FileNotFoundError + + # as the file checker can process a list of files from a given directory, + # we need to extract directories and files's names + # and launch files checker on each directory : + files_by_directory = self._get_filesnames_by_directory(existing_files) + + # for each directory, run the file checker on the associate list of files names : + validation_result_list = [] + for dir, files_names_list_in_dir in files_by_directory.items(): + validation_result_list.extend( + self._check_files_in_directory(dir, files_names_list_in_dir, dac_name, options) + ) + + return validation_result_list + + def _check_files_in_directory( + self, input_directory: Path, files_names: List[str], dac_name: str, options: list[str] + ) -> List[ValidationResult]: + """Run the file checker on a given directory and given files names. + + Args : + input_directory (Path) : the input directory Path + files_names (List[str]): List of files names in the directory + dac_name (str) : dac name of the files : coriolis, bodc, aoml, etc. Must be the same DAC for all files. + options (List[str]) : list of file checker options. ex: ['-no-name-check'] + + Returns : + A list of ValidationResult objects. + + """ + # need a temp directory for XML output + with tempfile.TemporaryDirectory(prefix="filechecker_output_") as temp_output_dir: + temp_output = Path(temp_output_dir) + + cmd = [ + "java", + "-jar", + str(self.jar_path), + *options, + dac_name, + str(self.specs_path), + str(temp_output), + str(input_directory), + *files_names, + ] + + # launch subprocess : + try: + result = subprocess.run(cmd, capture_output=True, text=True, check=False, timeout=300, shell=False) # nosec B603: no shell, fixed executable path + if result.stderr: + logger.error(result.stderr.strip()) + if result.stdout: + logger.info(result.stdout.strip()) + # parse xml results files + return self._parse_batch_results(temp_output, files_names) + + except subprocess.TimeoutExpired: + logger.exception("Timed out after 5 minutes") + raise RuntimeError + except Exception as e: + logger.exception("Failed to execute batch file checker") + raise RuntimeError from e + + def _parse_batch_results(self, temp_output_dir: Path, files_names: List[str]) -> List[ValidationResult]: + """Parse XML results files in the temp_ouput directory. + + For each result file build a ValidationResult and add it to the return list. + For each output file, parse the xml result and create a ValidationResult object and add it to the return list. + + Args : + temp_output (Path) : tempory folder to save XML output + input_directory (Path) : input directory path + files_names (List[str]) : list of files name that have been processed + + return : + A list of ValidationResult coming from the parsing of XML result files. + + """ + validation_results = [] + # get list of XML files : + xml_files = list(temp_output_dir.glob("*.filecheck")) + + if xml_files: + if len(xml_files) != len(files_names): + logger.warning("Unexpected number of output files") + + for xml_file in xml_files: + validation_result = self._parse_xml_output(xml_file) + if validation_result is not None: + validation_results.append(validation_result) + else: + logger.error("No results files were found") + + return validation_results + + def _parse_xml_output(self, xml_file: Path) -> ValidationResult | None: + """Parse a XML result file and build a ValidationResult object. + + Args : + xml_file (Path) : the xml file to be parsed + + Return : + an ValidationResult object + """ + try: + # Parsing XML file using defusedxml + tree: ElementTree[Element[str] | None] = DefusedET.parse(xml_file) # type: ignore[misc] + root: Element | None = tree.getroot() + + if root is None: + logger.error("Empty XML document: %s", xml_file) + return None + + def _extract_text(tag: str, default: str) -> str: + elem = root.find(tag) + if elem is not None and elem.text is not None: + return elem.text + else: + return default + + # file checker version + file_checker_version = root.attrib["filechecker_version"] + + # processed file's name + file = _extract_text("file", "") + + # result + result = _extract_text("status", "") + try: + result_enum = ResultType(result) if result else ResultType.ERROR + except ValueError: + result_enum = ResultType.ERROR + + # checking phase + phase = _extract_text("phase", "") + try: + phase_enum = PhaseType(phase) if result else PhaseType.FORMAT + except ValueError: + phase_enum = PhaseType.FORMAT + + # errors + errors_elem = root.find("errors") + if errors_elem is not None: + errors_number = errors_elem.attrib["number"] + errors_messages = list(errors_elem.itertext()) + else: + errors_number = "0" + errors_messages = [] + + # warnings + warnings_elem = root.find("warnings") + if warnings_elem is not None: + warnings_number = warnings_elem.attrib["number"] + warnings_messages = list(warnings_elem.itertext()) + else: + warnings_number = "0" + warnings_messages = [] + + validation_result = ValidationResult( + file_checker_version=file_checker_version, + file=str(file), + result=result_enum, + phase=phase_enum, + errors_number=int(errors_number), + warnings_number=int(warnings_number), + errors_messages=errors_messages, + warnings_messages=warnings_messages, + ) + + except ParseError: + logger.exception("Error when parsing file : " + str(xml_file)) + return None + + else: + return validation_result + + def _get_valid_files_path(self, files_paths_str: List[str]) -> tuple[list[Path], list[str]]: + """From a list of files, determinate for each file if it exist or not. + + Args : + files_paths_ str (list[str]) : list of files + + Return : + existing_files (List[Path]): list of existing files Path + missing_files (List[str]) : list of input files that don't exist. + """ + existing_files = [] + missing_files = [] + + for file_path_str in files_paths_str: + file_path = Path(file_path_str) + if file_path.exists(): + existing_files.append(file_path) + else: + missing_files.append(file_path_str) + + return existing_files, missing_files + + def _get_filesnames_by_directory(self, files_path: List[Path]) -> Dict[Path, List[str]]: + """Associate a source directory and list of files names from a list of files Path. + + Args : + files_path (list[Path]) : a list of files'path + + Return : + Dict[Path, List[str] : A dict with key : a directory's Path + and value : a list of files's names present in the directory. + """ + files_by_directory: Dict[Path, List[str]] = {} + for file_path in files_path: + parent_dir = file_path.parent + if parent_dir not in files_by_directory: + files_by_directory[parent_dir] = [] + files_by_directory[parent_dir].append(file_path.name) + + return files_by_directory diff --git a/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/models.py b/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/models.py new file mode 100644 index 0000000..2f61af5 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/src/argofilechecker_python_wrapper/models.py @@ -0,0 +1,42 @@ +"""Module defining data models and enums for the Argo file checker validation system.""" + +from enum import Enum +from typing import List + +from pydantic import BaseModel + + +class ResultType(str, Enum): + """Error codes possibilities.""" + + SUCCESS = "FILE-ACCEPTED" + FAILURE = "FILE-REJECTED" + ERROR = "ERROR" + + +class PhaseType(str, Enum): + """File Checker verification phases.""" + + OPEN_FILE = "OPEN-FILE" + FORMAT = "FORMAT-VERIFICATION" + DATA = "DATA-VALIDATION" + NAME = "FILE-NAME-CHECK" + + +class ValidationResult(BaseModel): + """Represents the result of an Argo file checker validation.""" + + file_checker_version: str + file: str + result: ResultType + phase: PhaseType + errors_number: int + warnings_number: int + errors_messages: List[str] + warnings_messages: List[str] + + def to_string(self) -> str: + """Summary for humans.""" + status = "FILE ACCEPTED" if self.result == ResultType.SUCCESS else "FILE REJECTED" + + return f"{self.file} : {status} with {self.errors_number} error(s) and {self.warnings_number} warning(s)" diff --git a/file_checker_python/file_checker_python_wrapper/tests/conftest.py b/file_checker_python/file_checker_python_wrapper/tests/conftest.py new file mode 100644 index 0000000..d97e8c3 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/tests/conftest.py @@ -0,0 +1,90 @@ +"""Fixtures for tests suite.""" + +import os +import shutil +import subprocess +from pathlib import Path + +import pytest +import requests + + +@pytest.fixture(scope="session") +def specs_directory(tmp_path_factory) -> Path: + """Fixture which download the up-to-date specs folder from the file checker git. + + Add it to the session context for tests 'data validation' suite. + Need to provide Argo file checker github repo informations. + """ + specs_repo_url = os.getenv("SPECS_REPO_URL", "https://github.com/OneArgo/ArgoFormatChecker.git") + ref = os.getenv("SPECS_REPO_REF", "main") # branch + specs_subdir = os.getenv("TEST_REPO_SUBDIR", "file_checker_spec/") # sub folder to extract + + dest = tmp_path_factory.mktemp("specs") # session wide folder to save specs files + + _clone_subdir(specs_repo_url, ref, specs_subdir, dest) # clone repo subdir in the dest directory + + return dest + + +@pytest.fixture(scope="session") +def file_checker_jar_file(tmp_path_factory) -> Path: + """Fixture to provide the file checker executable into the session context for tests 'data validation' suite.""" + jar_download_url = os.getenv( + "JAR_URL", "https://github.com/OneArgo/ArgoFormatChecker/releases/download/v2.9.3/file_checker_exec-2.9.3.jar" + ) + + dest = tmp_path_factory.mktemp("file_checker_exec") + # download file checker JAR : + _download(jar_download_url, dest, "app.jar") + + file_path = dest / "app.jar" + + return file_path + + +def _download(url: str, dest: Path, out_file_name: str, timeout: int = 120): + """Download file from provided url. + + Arg : + url (str) : url of the file + dest (Path) : destination folder + out_file_name (str) : name of the downloaded file in the dest folder + """ + file_path = dest / "app.jar" + # dowload the jar from the provide url + with open(dest / out_file_name, "wb") as out_file: + content = requests.get(url, stream=True).content + out_file.write(content) + + if not file_path.exists(): + raise FileNotFoundError(f"File checker jar not found at {file_path}") # noqa: TRY003 + + +def _clone_subdir(repo_url: str, branch: str, subdir: str, dest: Path): + dest.parent.mkdir(parents=True, exist_ok=True) + clone_dir = dest.parent / ".clone" + if clone_dir.exists(): + shutil.rmtree(clone_dir) + + # clone git repo : + cmd_clone = ["git", "clone", "--depth=1", "--filter=blob:none", "--sparse", repo_url, str(clone_dir)] + # change branch + cmd_checkout = ["git", "-C", str(clone_dir), "checkout", branch] + # Only subdir needed : + cmd_sparse_checkout = ["git", "-C", str(clone_dir), "sparse-checkout", "set", subdir] + # launch subprocesses : + subprocess.run(cmd_clone, cwd=None, check=True) + subprocess.run(cmd_checkout, cwd=None, check=True) + subprocess.run(cmd_sparse_checkout, cwd=None, check=True) + + # move sub folder to dest : + src = clone_dir / subdir + if not src.exists(): + raise FileNotFoundError(f"Directory '{subdir}' not found in {repo_url}@{branch}") # noqa: TRY003 + if dest.exists(): + shutil.rmtree(dest) + shutil.move(str(src), str(dest)) + + # Nettoyage du clone temporaire + shutil.rmtree(clone_dir, ignore_errors=True) diff --git a/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/3901682_tech_bad_long_name.nc b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/3901682_tech_bad_long_name.nc new file mode 100644 index 0000000..d5cb74b Binary files /dev/null and b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/3901682_tech_bad_long_name.nc differ diff --git a/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6903281_meta_PROGRAM_NAME_Not-in_ref-table-41.nc b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6903281_meta_PROGRAM_NAME_Not-in_ref-table-41.nc new file mode 100644 index 0000000..238db34 Binary files /dev/null and b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6903281_meta_PROGRAM_NAME_Not-in_ref-table-41.nc differ diff --git a/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6990661_meta_DOXY_2.nc b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6990661_meta_DOXY_2.nc new file mode 100644 index 0000000..818868c Binary files /dev/null and b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6990661_meta_DOXY_2.nc differ diff --git a/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6990728_tech_BadUnits.nc b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6990728_tech_BadUnits.nc new file mode 100644 index 0000000..e5fc2bc Binary files /dev/null and b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/6990728_tech_BadUnits.nc differ diff --git a/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/R6903129_088_QC0_TEMP.nc b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/R6903129_088_QC0_TEMP.nc new file mode 100644 index 0000000..0779f74 Binary files /dev/null and b/file_checker_python/file_checker_python_wrapper/tests/rejected_argo_data/R6903129_088_QC0_TEMP.nc differ diff --git a/file_checker_python/file_checker_python_wrapper/tests/test_argo_data_validation.py b/file_checker_python/file_checker_python_wrapper/tests/test_argo_data_validation.py new file mode 100644 index 0000000..6adf672 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/tests/test_argo_data_validation.py @@ -0,0 +1,103 @@ +"""Validation tests on real floats data.""" + +import os +from ftplib import FTP +from pathlib import Path +from typing import List +from urllib.parse import urlparse + +import pytest + +from argofilechecker_python_wrapper import FileChecker +from argofilechecker_python_wrapper.models import ResultType, ValidationResult + + +@pytest.mark.e2e +@pytest.mark.parametrize( + "float_number,dac_name", + [("2903996", "coriolis"), ("5900177", "bodc"), ("1900360", "aoml"), ("6990538", "coriolis"), ("4901791", "meds")], +) # noqa: E501 +def test_files_from_gdac_should_be_accepted(float_number, dac_name, tmp_path, specs_directory, file_checker_jar_file): + """Argo netcdf files from GDAC should be accepted.""" + # first download relevant files in temp directory : + ftp_url = os.getenv("GDAC_FTP_HOST", "ftp://ftp.ifremer.fr/ifremer/argo/dac") + dest_folder = tmp_path / float_number + dest_folder.mkdir() + _download_relevant_files_from_gdac_ftp(ftp_url, dac_name, float_number, dest_folder) + + # run file checker on each file and expect to have only accepted files + # Files come from GDAC and should be accepted by file checker + list_files = [f"{dest_folder}/{file}" for file in os.listdir(dest_folder)] + file_checker = FileChecker(file_checker_jar_file, specs_directory) + + results: List[ValidationResult] = file_checker.check_files(list_files, dac_name) + # check if all files have been processed + assert len(list_files) == len(results) + # check if all files are ACCEPTED (which is the expected result for GDAC files) + failures = [r.file for r in results if r.result != ResultType.SUCCESS] + assert not failures, f"REJECTED detected: {failures}" + + +@pytest.mark.e2e +def test_bad_argo_netcdf_should_be_rejected(specs_directory, file_checker_jar_file): + """Bad formatted argo netcdf should be rejected.""" + # files in local 'rejected_argo_data' folder : + test_dir = Path(__file__).parent + rejected_dir = test_dir / "rejected_argo_data" + list_files = [str(rejected_dir / file) for file in os.listdir(rejected_dir)] + # run file checker : + file_checker = FileChecker(file_checker_jar_file, specs_directory) + results: List[ValidationResult] = file_checker.check_files(list_files, "coriolis", ["-no-name-check"]) + # check if all files have been processed + assert len(list_files) == len(results) + # check if all files are REJECTED + success = [r.file for r in results if r.result == ResultType.SUCCESS] + assert not success, f"ACCEPTED detected: {success}" + + +def _download_relevant_files_from_gdac_ftp(ftp_url: str, dac_name: str, float_number: str, dest: Path): + """Download from a ftp server the different files (tech, meta, traj, profiles) for a specified dac and float number. + + Args : + ftp_url (str) : root directory where dac directories are found + dac_name (str) + float_number (str) + """ + # parse url to retrieve host and path + float_ftp_url = f"{ftp_url}/{dac_name}/{float_number}" + parsed_url = urlparse(float_ftp_url) + hostname = parsed_url.hostname + path = parsed_url.path + + # connect to ftp + if hostname is not None: + ftp = FTP(hostname) + ftp.login() + # go to the right folder : + ftp.cwd(path) + # download meta, traj and tech files : + meta_tech_traj_files_list = [f"{float_number}_Rtraj.nc", f"{float_number}_tech.nc", f"{float_number}_meta.nc"] + _download_files_from_ftp(ftp, meta_tech_traj_files_list, dest) + + # dowload profiles files : + ftp.cwd("profiles") + profiles_files_names = ftp.nlst() + # exclude Synthetic profiles (first letters is 'S') which are not checked by fileChecker + profiles_files_names_without_synth = [f for f in profiles_files_names if not f.startswith("S")] + _download_files_from_ftp(ftp, profiles_files_names_without_synth, dest) + + ftp.quit() + + +def _download_files_from_ftp(ftp, files_names_list, dest): + """Download a list of files to a dest directory from a FTP connexion. + + Args : + ftp (FTP) : FTP object (ftplib) connected to the right directory + files_names_list (List[str]) : list of file names present in the ftp directory + dest (Path) : Path of the directory to download files + """ + for file_name in files_names_list: + if file_name in ftp.nlst(): + with open(dest / file_name, "wb") as fp: + ftp.retrbinary(f"RETR {file_name}", fp.write) diff --git a/file_checker_python/file_checker_python_wrapper/tests/test_filechecker.py b/file_checker_python/file_checker_python_wrapper/tests/test_filechecker.py new file mode 100644 index 0000000..c57c8ba --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/tests/test_filechecker.py @@ -0,0 +1,34 @@ +"""Tests for the argofilechecker_python_wrapper module.""" + +import pytest + +from argofilechecker_python_wrapper import FileChecker + + +@pytest.fixture +def env_paths(tmp_path, monkeypatch): + """Create a mock JAR file and specs dir and add it to env variables.""" + jar = tmp_path / "app.jar" + jar.touch() # simulate jar existence + specs = tmp_path / "specs" + specs.mkdir() + + monkeypatch.setenv("FILE_CHECKER_JAR", str(jar)) + monkeypatch.setenv("FILE_CHECKER_SPECS", str(specs)) + return jar, specs + + +def test_check_files_empty_input_files_list(env_paths): + """Should raise an Error when no files list are provided.""" + file_checker = FileChecker() + + with pytest.raises(ValueError): + file_checker.check_files([], "coriolis") + + +def test_check_files_all_missing_raise(env_paths): + """Should raise an error when a file provided doesn't exists.""" + file_checker = FileChecker() + + with pytest.raises(FileNotFoundError): + file_checker.check_files(["NOEXISTS.nc"], "coriolis") diff --git a/file_checker_python/file_checker_python_wrapper/tox.ini b/file_checker_python/file_checker_python_wrapper/tox.ini new file mode 100644 index 0000000..43fcc05 --- /dev/null +++ b/file_checker_python/file_checker_python_wrapper/tox.ini @@ -0,0 +1,64 @@ +[base] +# Name of the Python package we're going to run jobs against +name = argofilechecker_python_wrapper + +[tox] +minversion = 4.23.2 + +# Use Python as provided by our environment. +ignore_basepython_conflict = true + +# Which envs to run when Tox is called with no args. +envlist = test, test_e2e, build, lint, bandit, type + +[testenv:test] +setenv = PYTHONPATH = {toxinidir}/src +# Our primary base environment for all jobs. +extras = test +allowlist_externals = + coverage + pytest +commands = + coverage run -m --source {[base]name} --data-file=coverage_reports/.coverage --omit tests/* pytest -m "not e2e" + coverage xml --data-file=coverage_reports/.coverage -o coverage_reports/coverage.xml + coverage report --data-file=coverage_reports/.coverage -m + +[testenv:test_e2e] +description = end-to-end tests downloading data from GDAC +setenv = PYTHONPATH = {toxinidir}/src +extras = test +allowlist_externals = + pytest +commands = + pytest -m "e2e" -s + +[testenv:lint] +# Linting with Ruff. +allowlist_externals = ruff +extras = lint +commands = + ruff check --fix src/{[base]name} + +[testenv:bandit] +# Security checks with bandit. +allowlist_externals = bandit +extras = bandit +commands = + bandit -r src/{[base]name} -c pyproject.toml + +[testenv:type] +# Type-checking with Mypy. +allowlist_externals = mypy +extras = type +commands = + mypy src/{[base]name} + +[testenv:build] +# Package building with Poetry and Twine. +allowlist_externals = + poetry + twine +extras = build +commands = + poetry build + twine check dist/* diff --git a/file_checker_spec/ref_table-27 b/file_checker_spec/ref_table-27 index 3a35f1d..c3c373a 100644 --- a/file_checker_spec/ref_table-27 +++ b/file_checker_spec/ref_table-27 @@ -65,13 +65,13 @@ SBE61_V5.0.9 | SBE | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | 2021-12-10 | added SBE61_V5.0.10 | SBE | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | 2023-07-21 | https://github.com/nvs-vocabs/ArgoVocabs/issues/65 SBE61_V5.0.12 | SBE | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | 2023-07-21 | https://github.com/nvs-vocabs/ArgoVocabs/issues/65 CTD_F01 | TSK | TSK model | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | | -RBR | RBR | RBR model | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | | +RBR | RBR | RBR model | CTD_PRES, CTD_TEMP, CTD_CNDC, CTD_TEMP_CNDC | CTD | | RBRoem_V1.16 | RBR | RBR model | CTD_PRES, CTD_TEMP, CTD_CNDC | | | deprecated -RBR_ARGO | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 -RBR_ARGO3 | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 -RBR_ARGO3_DEEP4K | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 -RBR_ARGO3_DEEP6K | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 -RBR_CTD | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC | CTD | 2025-09-23 | added by ylubac 23/09/2025 https://github.com/OneArgo/ArgoVocabs/issues/157 +RBR_ARGO | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC, CTD_TEMP_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 +RBR_ARGO3 | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC, CTD_TEMP_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 +RBR_ARGO3_DEEP4K | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC, CTD_TEMP_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 +RBR_ARGO3_DEEP6K | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC, CTD_TEMP_CNDC | CTD | | added by MB 15/07/2020 completed by VT 28/07/2020 +RBR_CTD | RBR | | CTD_PRES, CTD_TEMP, CTD_CNDC, CTD_TEMP_CNDC | CTD | 2025-09-23 | added by ylubac 23/09/2025 https://github.com/OneArgo/ArgoVocabs/issues/157 //Oxygen sensors | | | | | | RBR_CODA_T_ODO | RBR | | OPTODE_DOXY | OPTODE | | added by VT 28/07/2020 diff --git a/python.Dockerfile b/python.Dockerfile new file mode 100644 index 0000000..0ab8fc9 --- /dev/null +++ b/python.Dockerfile @@ -0,0 +1,106 @@ +FROM ghcr.io/oneargo/argoformatchecker/app:develop AS base + +USER root + +# Install Poetry for dependency management. +ENV POETRY_HOME=/opt/poetry +ENV PATH="${POETRY_HOME}/bin:${PATH}" + +RUN \ + apk add --no-cache \ + python3 \ + py3-pip \ + curl \ + build-base \ + python3-dev \ + git && \ + ln -sf /usr/bin/python3 /usr/bin/python && \ + mkdir -p /opt/poetry/project /opt/poetry/bin && \ + curl -sSL https://install.python-poetry.org | python - + +# Install dependencies. +COPY file_checker_python/file_checker_python_wrapper/pyproject.toml file_checker_python/file_checker_python_wrapper/poetry*.lock file_checker_python/file_checker_python_wrapper/README.md /opt/poetry/dep/ +RUN \ + cd /opt/poetry/dep && \ + poetry config virtualenvs.create false && \ + if [ ! -f poetry.lock ]; then poetry lock; fi && \ + poetry install --no-root && \ + poetry env info + +FROM base AS build-package +# Ephemeral environment for building packages. +RUN --mount=type=bind,source=./file_checker_python/file_checker_python_wrapper,target=/opt/dep,rw=true \ + cd /opt/dep && \ + rm -rf ./dist && \ + POETRY_DYNAMIC_VERSIONING_BYPASS=1.0.0 poetry build && \ + mkdir /opt/build && \ + mv ./dist/*.whl /opt/build + +FROM base AS file-checker-python + +LABEL org.opencontainers.image.authors="yvan.lubac@euro-argo.eu" +LABEL org.opencontainers.image.description="Docker image for Argo File Checker Python Wrapper" +LABEL org.opencontainers.image.url="https://github.com/British-Oceanographic-Data-Centre/amrit-repos" +LABEL org.opencontainers.image.source="https://github.com/British-Oceanographic-Data-Centre/amrit-repos" +LABEL org.opencontainers.image.documentation="https://github.com/British-Oceanographic-Data-Centre/amrit-repos/wiki" +LABEL org.opencontainers.image.licenses="TBD" +LABEL org.opencontainers.image.vendor="Advance Marine Research Infrastructures Together (AMRIT)" + +COPY ./file_checker_spec /app/specs + +#env variables for file checker +ENV FILE_CHECKER_JAR="/app/app.jar" +ENV FILE_CHECKER_SPECS="/app/file_checker_spec" + +RUN --mount=type=bind,from=build-package,source=/opt/build,target=/opt/build \ + python -m venv /opt/venv && \ + /opt/venv/bin/pip install /opt/build/*.whl && \ + /opt/venv/bin/python -c "from argofilechecker_python_wrapper import FileChecker; print('OK')" + + +ENV PATH="/opt/venv/bin:${PATH}" + +WORKDIR /home/app + +USER fileCheckerRunner + +#overide entrypoint from base image +ENTRYPOINT ["/opt/venv/bin/python"] + +FROM base AS file-checker-api + +LABEL org.opencontainers.image.description="Docker image for Argo File Checker Python API" +LABEL org.opencontainers.image.url="https://github.com/British-Oceanographic-Data-Centre/amrit-repos" +LABEL org.opencontainers.image.source="https://github.com/British-Oceanographic-Data-Centre/amrit-repos" + +#env variables for file checker +ENV FILE_CHECKER_JAR="/app/app.jar" +ENV FILE_CHECKER_SPECS="/app/file_checker_spec" +ENV UPLOAD_FILES_DIR="/home/app/input" + +WORKDIR /home/app +COPY file_checker_python/file_checker_python_api/pyproject.toml file_checker_python/file_checker_python_api/poetry*.lock file_checker_python/file_checker_python_api/README.md ./ + +RUN --mount=type=bind,from=build-package,source=/opt/build,target=/opt/build \ + python -m venv /opt/venv && \ + /opt/venv/bin/pip install /opt/build/*.whl && \ + /opt/venv/bin/python -c "from argofilechecker_python_wrapper import FileChecker; print('OK')" + +RUN --mount=type=bind,from=build-package,source=/opt/build,target=/opt/build \ + poetry config virtualenvs.create false && \ + poetry add /opt/build/*.whl && \ + if [ ! -f poetry.lock ]; then poetry lock; fi && \ + poetry install --no-root && \ + poetry env info + +COPY file_checker_python/file_checker_python_api/ ./ + +ENV PATH="/opt/venv/bin:${PATH}" +RUN mkdir /home/app/input +RUN chown fileCheckerRunner:gcontainer /home/app/input + +USER fileCheckerRunner + +#overide entrypoint from base image +ENTRYPOINT ["poetry"] +CMD ["run", "gunicorn", "file_checker_api:app", "-b", "0.0.0.0:8000", "-k", "uvicorn.workers.UvicornWorker", "--timeout", "300"] diff --git a/python.README.md b/python.README.md new file mode 100644 index 0000000..87898b2 --- /dev/null +++ b/python.README.md @@ -0,0 +1,93 @@ +# ArgoFileChecker Python Wrapper + +A lightweight Python wrapper around the **Argo NetCDF File Checker**. +It runs the File Checker JAR as a **subprocess**, parses the generated XML output files (which are generated in a temporary folder), and returns typed `ValidationResult` objects. + +## Installation + +### With Poetry + +```bash +cd ./file_checker_python/file_checker_python_wrapper +poetry install +``` + +## Run ArgoFileChecker Python Wrapper (after installing the package and any additional dependencies) +The wrapper can receive paths explicitly or through environment variables: + +FILE_CHECKER_JAR: path to file_checker_exec-*.jar + +FILE_CHECKER_SPECS: path to the file_checker_spec directory + +### Usage example +See /demo_scripts where a demo python script is provided along with a file checker .jar and some netcdf test data. + +```bash +cd ./demo_scripts +poetry run python demo_test.py +``` + +## Run ArgoFileChecker Python Wrapper in a pre-built container image + +### build and run the image + +```bash +docker build --target file-checker-python -f python.Dockerfile -t argofilechecker-python:latest . +``` + +Argo File checker .jar file will be included in the docker image but you still need to mount your data your script file (if not used in interactive mode) : + +```bash +docker run --rm -v ${pwd}/file_checker_python/file_checker_python_wrapper/demo_scripts/demo_docker.py:/scripts/demo_docker.py -v ${pwd}/demo/inputs/2903996:/data argofilechecker-python:latest /scripts/demo_docker.py +``` +Ensure that the correct volumes names are used in your script. + +You can use interactive mode to execute python code inside the container : + +```bash +docker run --rm -it -v ${pwd}/demo/inputs/2903996:/data argofilechecker-python:latest +>>> from argofilechecker_python_wrapper import FileChecker +>>> filechecker = FileChecker() +>>> results = filechecker.check_files(['/data/2903996_meta.nc'],"coriolis") +>>> results[0].to_string() +'/data/2903996_meta.nc : FILE ACCEPTED with 0 error(s) and 0 warning(s)' +``` + + +### Results Values + +- ResultType.SUCCESS → the file is accepted by the File Checker. + +- ResultType.FAILURE → the file is rejected (errors found). + +- ResultType.ERROR → internal error in the checker or parsing failure. + +The phase (PhaseType) indicates the stage where the error occurred: opening, format check, data validation, or file name check. + +Errors and warnings's number and messages can be accessed also. + +For more information see models.py + +# Argo File Checker Python API + +A FastAPI app providing an endpoint to access file checker functionality via the /check-files endpoint. + +## Build and run using Docker + +```bash +docker build --target file-checker-api -f python.Dockerfile -t argofilechecker-api:latest . +docker run -p 8000:8000 argofilechecker-api:latest +``` + +The file checker endpoint will then be available on http://localhost:8000/check-files +API documentation can be found on http://localhost:8000/docs + +The DAC for the files needs to be specified as a parameter. The files to check need to be included in the body of a `multipart/form-data` type request, e.g.: +For example, post an example file found in the _argofilechecker-python-wrapper/demo_scripts/test_data/2903996_ folder to `http://localhost:8000/check-files?dac=coriolis` +```http request +curl -X 'POST' \ + 'http://localhost:8000/check-files?dac=coriolis' \ + -H 'accept: application/json' \ + -H 'Content-Type: multipart/form-data' \ + -F 'files=@2903996_meta.nc' +```