gn2pg_client 1.9.1

Import tool from GeoNature to a PostgreSQL database through Export module API (client side)

GN2PG Client

This project provides an import data from GeoNature instances to a PostgreSQL database (client side). Widely inspired from ClientApiVN

[!WARNING] The minimum version of the source GeoNature instance required for the incremental update must be a version 2.12.0

Project Setup

GN2PG Client can be installed by running pip. It requires Python 3.9 or above to run.

pip install gn2pg-client

Issues

Please report any bugs or requests that you have using the GitHub issue tracker!

HowTo

Help

gn2pg_cli --help

Init config file

This command init a TOML config file within ~/.gn2pg hidden directory (in user HOME directory), named as you want. PLEASE DO NOT SPECIFY PATH!

gn2pg_cli config --init <myconfigfile>

Config file is structured as this. [[source]] block can be duplicate as many as needed (one block for each source).

The data_type value on each source is used to characterize the type of data. This value is used to identify which triggers to be triggered when inserting, updating or deleting data. Current provided trigger configs are:

• synthese_with_cd_nomenclature which provide triggers to insert basically data on synthese and generate basic metadatas (acquisition framework and datasets). Source query sample is provided in file geonature_export_sinp_with_cd_nomenclature.sql
• synthese_with_metadata which provide triggers to insert data in synthese and populate most of the metadata data (acquisition frameworks, datasets, actors such as organisms and roles, territories, etc.). Source query sample is provided in file geonature_export_sinp_with_metadata.sql

# GN2PG configuration file

# Local db configuration
[db]
db_host = "localhost"
db_port = 5432
db_user = "<dbUser>"
db_password = "<dbPassword>"
db_name = "<dbName>"
db_schema_import = "schema"
    # Additional connection options (optional)
    [db.db_querystring]
    sslmode = "prefer"


# Source configuration,
# Ducplicate this block for each source (1 source = 1 export)
[[source]]
# Source name, will be use to tag stored data in import table
name = "Source1"
# GeoNature source login
user_name = "<monuser>"
# GeoNature source password
user_password = "<monPwd>"
# GeoNature source URL
url = "<http://geonature1/>"
# GeoNature source Export id
export_id = 1
# Data type is facultative. By default the value is 'synthese'. Therefore, triggers from to_gnsynthese.sql are not activated.
# If you want to insert your data into a GeoNature database please choose either 'synthese_with_cd_nomenclature' or 'synthese_with_metadata'.
# If not, delete the line.
data_type = "synthese_with_cd_nomenclature"


[[source]]
# Source configuration
name = "Source2"
user_name = "<monuser>"
user_password = "<monPwd>"
url = "<http://geonature2/>"
export_id = 1
data_type = "synthese_with_cd_nomenclature"

[!TIP] You can add variable in source block enable = false to disable a source

InitDB Schema and tables

To create json tables where datas will be stored, run :

gn2pg_cli db --json-tables-create <myconfigfile>

Full download

To download all datas from API, run :

gn2pg_cli download --full <myconfigfile>

Incremental download

To update data since last download, run :

gn2pg_cli download --update <myconfigfile>

To automate the launching of updates, you can write the cron task using the following command, for example every 30 minutes.

*/30 * * * * /usr/bin/env bash -c "source <path to python environment>/bin/activate && gn2pg_cli download --update <myconfigfile>" > /dev/null 2>&1

Debug mode

Debug mode can be activated using --verbose CLI argument

Logs

Log files are stored in $HOME/.gn2pg/log directory.

Import datas into GeoNature database

Default script to auto populate GeoNature is called "to_gnsynthese".

gn2pg_cli db --custom-script to_gnsynthese <myconfigfile>

[!TIP] You can also replacing synthese script by your own scripts, using file path instead of to_gnsynthese.

Dashboard

A simple web dashboard can be run following dashboard docs.

Contributing

All devs must be done in forks (see GitHub doc).

Pull requests must be pulled to dev branch.

Install project and development requirements (require poetry):

poetry install --with=docs --all-extras
poetry run pre-commit install

Make your devs and pull requests.

Test gn2pg_cli in dev mode by running this command:

poetry run gn2pg_cli <options>

Licence

GNU AGPLv3

Team

@lpofredc (LPO Auvergne-Rhône-Alpes), lead developer

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With the financial support of the DREAL Auvergne-Rhône-Alpes and the Office français de la biodiversité.