Update/table27 rbr ctd temp cndc

.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
 

.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
 

.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=<path to the file_checker_spec directory>
 FILECHECKER_INPUT_VOLUME=<path to input directory>
 FILECHECKER_OUTPUT_VOLUME=<path to output directory>
 

.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

.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

.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

.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"

file_checker_exec/Dockerfile → 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"]
 

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

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}

file_checker_exec/pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>fr.ifremer</groupId>
 	<artifactId>file_checker_exec</artifactId>
-	<version>2.9.3</version>
+	<version>2.9.4</version>
 
 	<name>Argo NetCDF file format checker</name>
 

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));
 			}
 
 		}

file_checker_python/file_checker_python_api/file_checker_api/__init__.py

@@ -0,0 +1 @@
+from .app import app

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