update_vn Documentation

User Guide

Caution

This application changes or deletes items directly in the Biolovision database. Use with extreme care !

The application update_vn reads an input CSV file containing operations to be applied to the Biolovision database. Each line of this file describes an operation.

Initial setup

Initialize the sample YAML file in your HOME directory and edit with your local details. The YAML file is self documented:

update_vn --init .evn_your_site.yaml
editor $HOME/.evn_your_site.yaml

CSV file content

The CSV file must start with the mandatory first line with column headers:

site;id_universal;path;operation;value

The next lines must contain the following columns:

site, as defined in YAML site section
id_universal of the sighting to be modified
path to the attribute to modify, in JSONPath syntax, unused if operation is delete_observation
operation:
- replace: create, if this attibute is not present, or update a sighting attribute
- delete_attribute: remove the attribute with the given path and keep the other attributes of the observation
- delete_observation, to remove completely the observation
value: if operation is replace, new value inserted or updated

Note: each operation is logged in hidden_comment, as a JSON message. It is not possible to replace hidden_comment, as logging is appended.

For example:

site;id_universal;path;operation;value
Isère;2246086;$['data']['sightings'][0]['observers'][0]['atlas_code'];replace;4
Isère;2246086;$['data']['sightings'][0]['observers'][0]['atlas_code'];delete_attribute;
Isère;2246086;;delete_observation;

Running the application

The application runs as:

update_vn options config input

where:

options  command line options described below
config   YAML file, located in $HOME directory, described in sample file
input    CSV file listing sightings to be updated

-h, --help: Prints help and exits
--version: Print version number
--verbose: Increase output verbosity
--quiet: Reduce output verbosity
--init: Initialize the YAML configuration file

Operations Templates

The following examples can be used as templates:

Modification du code projet

La liste des projets est accessible sur le site faune-xxx, dans “Administration” > “Gestion de projet” Attention, le numéro de projet est spécifique à chaque site:

site;id_universal;path;operation;value
Isère;2775784;$['data']['sightings'][0]['observers'][0]['project'];replace;6

Modification de l’utilisateur

Il faut modifier à la fois :

traid : transmitter id
@id : observer id

Il est possible de ne pas modifier le paramètre traid dans le cas de données intégrées via un compte d’archives par exemple pour conserver le fait que la donnée a été importée:

site;id_universal;path;operation;value
Isère;2775784;$['data']['sightings'][0]['observers'][0]['@id'];replace;38
Isère;2775784;$['data']['sightings'][0]['observers'][0]['traid'];replace;38

Ajout d’un commentaire

Attention, texte entre guillemets simples:

site;id_universal;path;operation;value
Isère;2775784;$['data']['sightings'][0]['observers'][0]['comment'];replace;'test'

Changement de comptage

Remplacement de “non compté” par un compte exact:

site;id_universal;path;operation;value
Isère;2775784;$['data']['sightings'][0]['observers'][0]['estimation_code'];replace;'EXACT_VALUE'
Isère;2775784;$['data']['sightings'][0]['observers'][0]['count'];replace;1

Changement de la date

La date est défine par timestamp calculé par la fonction Excel =(C2-DATE(1970;1;1))*86400:

site;id_universal;path;operation;value
Isère;2775784;$['data']['sightings'][0]['date']['@timestamp'];replace;1465948800

Mortalité

Ajout de la mortalité avec une cause:

site;id_universal;path;operation;value
Isère;2775784;$['data']['sightings'][0]['observers'][0]['has_death'];replace;2
Isère;2775784;$['data']['sightings'][0]['observers'][0]['extended_info']['mortality']['death_cause2'];replace;'ROAD_VEHICLE'

Espèce

Modification en utilisant le numéro de l’espèce sur la plateforme concernée:

site;id_universal;path;operation;value
vn26;1399774;$['data']['sightings'][0]['species']['@id'];replace;'370'