easyqcvbgc/easy-qcv_odv-history-manager_tool

Repository overview

General presentation

This tool reports user action performed with ODV (EDITDATA and EDITFLAGS) in the original standardized dataset in an automatic way.

ODV user guides : [***]

Version capabilities

This latest version oh1.2 is available for x86 linux

oh1.2 better managment of the file names 1.1 to debug galaxy functionalities

How to use

To use this tool,

1. install docker (https://docs.docker.com/engine/install/)
2. run the command as explained below

Quick Demo

wget https://gitlab.com/pokapok-showcase/demo-launchers/-/raw/main/qcv_odv_history_manager_launch.sh && chmod +x qcv_odv_history_manager_launch.sh && ./qcv_odv_history_manager_launch.sh

Run example To run the tool, fill this command with your configuration :

docker run \
    -v <config_path>:/runtime/config \
    -v <raw_data_path>:/runtime/data-in-raw \
    -v <history_data_path>:/runtime/data-in-history \
    -v <log_path>:/runtime/log \
    -v <output_path>:/runtime/data-out \
    -e FORCE_USER_ID=$(id -u) \
    -e FORCE_GROUP_ID=$(id -g) \
    -e demo=0 \
    easyqcvbgc/easy-qcv_odv-history-manager_tool:latest \
    /app/launchers/start-app.sh

with :

• a config file named config_user_odv_manager.yml with mandatory and optional information (see below a example)
• paths of where are the data (volumes) containing configurations, listings and data. Paths are :
  • config path : where config_user_odv_manager.yml is stored
  • raw_data_path : the folder where data nc file_name_raw are stored
  • history_data_path : the folder where data txt file_name_history coming from ODV are stored and the odv collection used
  • log_path : the folder where to write the log file. This log summarizes tool actions
  • output_path : the folder where to write qced raw nc file (file_name_raw_qced).
  • MODE : R_APP_QV that creates a odv collection with raw and ref files
• demo (optional) environment information : 0 (by default) or 1

If you do not want to mounted a volume, comment the corresponding "-v"

config_user_odv_tool.yml description

default :
#mandatory information
    file_name_list_raw :
        - file_name_raw_1.nc
        - file_name_raw_2.nc
        - file_name_raw_3.nc     
#optional
    operator : name_or_email_of_the_operator
history : 
    odv_collection :
        name : odv_collection_de_toto.txt
        qc_convention : qc_convention_for_the_odv_collection
    file_name_odv_history : 
        - file_name_history_1
        - file_name_history_2
    change_report : # choose the change report 
        - EDITFLAGS
        - EDITDATA

with:

• file_name_raw : nc file to be qualified
• file_name_history : history txt file extracted from ODV (manualy or automatically)
• odv_collection$name : name of the odv collection view with webODV and updated
• odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw

with default values different from NULL :

• odv_collection$name : odv_collection.txt
• odv_collection$qc_convention : ARGO
• tool_action :
• tool_option$subsetting :
• tool_option$plt :

If the list of raw or history file name is e***y, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-history

Acknowledgements

This tool was made in the framework of the Horizon Europe project fair-ease (grant agreement number: ***).