Demonstration files to run format checker with Docker

.env.demo.bodc

@@ -0,0 +1,14 @@
+# 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=./file_checker_spec
+FILECHECKER_INPUT_VOLUME=./demo/inputs/3901945
+FILECHECKER_OUTPUT_VOLUME=./demo/outputs/3901945
+
+# Variable specific to floats to check
+DAC_NAME=bodc
+FILECHECKER_OPTIONS=
+FILES_NAMES=

.env.demo.coriolis

@@ -0,0 +1,14 @@
+# 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=./file_checker_spec
+FILECHECKER_INPUT_VOLUME=./demo/inputs/2903996_coriolis
+FILECHECKER_OUTPUT_VOLUME=./demo/outputs/2903996_coriolis
+
+# Variable specific to floats to check
+DAC_NAME=coriolis
+FILECHECKER_OPTIONS=
+FILES_NAMES=

.env.docs

@@ -13,3 +13,6 @@ 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>
 
+# Variable specific to Docker
+DOCKER_UID=<user uid for output files>
+DOCKER_GID=<user git for output files>

.gitignore

@@ -0,0 +1,4 @@
+demo/outputs/*
+.env
+
+!.gitkeep

README.md

@@ -1,60 +1,73 @@
 # Argo NetCDF file format checker
+
 The Argo NetCDF file format checker performs format and content checks on Argo NetCDF files.  
-The Argo NetCDF format is described in "Argo user's manual" http://dx.doi.org/10.13155/29825  
-More information on https://www.argodatamgt.org/Documentation  
+The Argo NetCDF format is described in "Argo user's manual" <http://dx.doi.org/10.13155/29825>  
+More information on <https://www.argodatamgt.org/Documentation>  
 The format checker has two directories:
+
 - file_checker_exec : the java code
 - file_checker_spec : the rules applied on the NetCDF file by the java code
 
 The rules files implement the Argo vocabularies managed on [NVS vocabulary server](https://vocab.nerc.ac.uk/search_nvs/).  
 Vocabularies and format changes are managed on [Argo Vocabs Task Team - AVTT GitHub](https://github.com/orgs/OneArgo/projects/4/views/1).
 
 **With each release (from 2.9.2) you will find :**
+
 - **file_checker_exec-[version].jar** which consolidates both application's compiled code and all its dependencies into a single executable file.
-- source code 
+- source code
 
 ## Run Argo NetCDF file format checker
+
 ### Using file_checker_exec-{version}.jar :
+
 ```bash
 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.
 
 ### 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
+[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
+
+```bash
 docker compose -f compose.yaml up
 ```
+
 or in background :
 
 ```bash
 docker compose -f compose.yaml up -d
 ```
-Example of an .env file : 
-```
+
+Example of an .env file :
+
+```text
 # file checker image
 FILECHECKER_IMAGE=ghcr.io/oneargo/argoformatchecker/app
 FILECHECKER_IMAGE_TAG=develop
@@ -68,9 +81,28 @@ FILECHECKER_OUTPUT_VOLUME='D:\test_compose\results'
 DAC_NAME=bodc
 FILECHECKER_OPTIONS=
 FILES_NAMES=
+```
+
+### Run the application on demonstration files
+
+Demonstration data are availables to run the application locally easily.
 
+- Clone the repository :
+
+```bash
+git clone https://github.com/OneArgo/ArgoFormatChecker.git
 ```
-### Test data :
+
+- Run the script dedicated
+
+```bash
+./run-file-checker-linux.sh
+```
+
+output files will be generated in `./demo/outputs`.
+
+### 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.
@@ -93,26 +125,23 @@ git clone https://github.com/OneArgo/ArgoFormatChecker.git
 
 - Build the application with maven (will requiert Java jdk installed), in file_checker_exec folder :
 
-
 ```bash
 cd file_checker_exec
 ./mvnw clean install
 ```
 
 In target folder you will find both original-file_checker_exec and file_checker_exec-[version]. It is this last one to use.
 
-
 ### build docker image
 
-
 - Build the application with Docker :
 
-```
+```bash
 docker build -t filechecker_2.8.14 .
 ```
 
-
 ### Run integration tests
+
 The source code comes with some netcdf test files. You can run the integration tests with this following command :
 
 ```bash

compose.yaml

@@ -2,8 +2,9 @@ services:
   argo-netcdf-checker:
     container_name: ArgoFormatChecker
     image: ${FILECHECKER_IMAGE}:${FILECHECKER_IMAGE_TAG}
-    env_file:
-      - .env
+    user: "${DOCKER_UID:-0}:${DOCKER_GID:-0}"
+    group_add:
+      - 1001
     volumes:
       - ${FILECHECKER_SPEC_VOLUME}:/app/file_checker_spec:ro
       - ${FILECHECKER_INPUT_VOLUME}:/app/data:ro

run-file-checker-linux.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# TODO : add when container can run as non root
+# export DOCKER_UID=$UID
+# export DOCKER_GID=$(id -g $UID)
+
+docker compose --env-file .env.demo.bodc down
+docker compose --env-file .env.demo.bodc up