update readme and provide compose.yaml to run filechecker with docker compose

Author: YvanEuroArgo

.env.docs

@@ -0,0 +1,15 @@
+# file checker image
+FILECHECKER_IMAGE=ghcr.io/oneargo/argoformatchecker/app
+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>
+
+# Variable specific to floats to check
+DAC_NAME=<The dac name for the file to check>
+FILECHECKER_OPTIONS=<optional list of options>
+FILES_NAMES=<optional list of file names to process>
+

README.md

@@ -14,12 +14,65 @@ Vocabularies and format changes are managed on [Argo Vocabs Task Team - AVTT Git
 - source code 
 
 ## Run Argo NetCDF file format checker
-- Using file_checker_exec-[version].jar :
+### Using file_checker_exec-{version}.jar :
 ```bash
-java -jar file_checker_exec-[version].jar $OPTION $DAC_NAME $SPEC $OUTPUT_DIR $INPUT_DIR $FILE_NAME
+java -jar file_checker_exec-{version}.jar $OPTION $DAC_NAME $SPEC $OUTPUT_DIR $INPUT_DIR [$FILES_NAMES]
 ```
+$FILES_NAMES is a list of file's name from the INPUT_DIR. It is optional : without it, all files from INPUT_DIR will be checked.
 
-Only this JAR file is needed. You can delete legacy log4j2 & netcdf libraries jar files.
+### Run the application using Docker
+
+```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} $DAC_NAME ./file_checker_spec ./results ./data [$FILES_NAMES]
+```
+You need to mount external directories to the container :
+
+[ABSOLUTE_PATH_TO_SPEC] : the file_checker_spec directory path.
+
+[ABSOLUTE_PATH_TO_DATA_FOLDER] : Path to directory containing the argo necdf files to be checked. The fileChecker will not seek files in subfolders
+
+[ABSOLUTE_PATH_TO_OUTPUT_DIR] : the directory where xml results files *.filecheck will be created
+
+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
+```
+
+### Run the application using Docker Compose
+To facilitate the use of Argo file checker a compose.yaml and .env files are provided :
+
+- Prepare your data.
+- Copy `.env.docs` as `.env` file, and customize variables to configure the file checker for your environment.
+- Download compose.yaml
+- Run te service using Docker Compose:
+ ```bash
+docker compose -f compose.yaml up
+```
+or in background :
+
+```bash
+docker compose -f compose.yaml up -d
+```
+Example of an .env file : 
+```
+# file checker image
+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'
+
+# Variable specific to floats to check
+DAC_NAME=bodc
+FILECHECKER_OPTIONS=
+FILES_NAMES=
+
+```
+### Test data :
+To 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.
 
 ## TOOLS
 
@@ -48,7 +101,7 @@ cd file_checker_exec
 In target folder you will find both original-file_checker_exec and file_checker_exec-[version]. It is this last one to use.
 
 
-### Using docker
+### build docker image
 
 
 - Build the application with Docker :
@@ -57,11 +110,6 @@ In target folder you will find both original-file_checker_exec and file_checker_
 docker build -t filechecker_2.8.14 .
 ```
 
-- Run the application using Docker
-
-```
-docker run --rm -v [ABSOLUTE_PATH_TO_file_checker_spec]:/app/file_checker_spec -v [ABSOLUTE_PATH_TO_DATA_FOLDER]:/app/data -v [ABSOLUTE_PATH_TO_OUTPUT_DIR]:/app/results filechecker_2.8.14:latest $DAC_NAME ./file_checker_spec ./results ./data $FILE_NAME
-```
 
 ### Run integration tests
 The source code comes with some netcdf test files. You can run the integration tests with this following command :

compose.yaml

@@ -0,0 +1,11 @@
+services:
+  argo-netcdf-checker:
+    container_name: ArgoFormatChecker
+    image: ${FILECHECKER_IMAGE}:${FILECHECKER_IMAGE_TAG}
+    env_file:
+      - .env
+    volumes:
+      - ${FILECHECKER_SPEC_VOLUME}:/app/file_checker_spec:ro
+      - ${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/Dockerfile

@@ -1,5 +1,14 @@
 FROM eclipse-temurin:21-jdk-alpine AS builder
 
+LABEL org.opencontainers.image.authors="yvan.lubac@euro-argo.eu"
+LABEL org.opencontainers.image.description="Docker Image for Argo netcdf File Checler"
+LABEL org.opencontainers.image.url="https://github.com/OneArgo/ArgoFormatChecker"
+LABEL org.opencontainers.image.source="https://github.com/OneArgo/ArgoFormatChecker"
+LABEL org.opencontainers.image.documentation="https://github.com/OneArgo/ArgoFormatChecker"
+LABEL org.opencontainers.image.licenses="TBD"
+LABEL org.opencontainers.image.vendor="OneArgo"
+
+
 WORKDIR /build
 
 COPY ./.mvn ./.mvn