update_vn Documentation¶
User Guide¶
Warning
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 TOML file in your HOME directory and edit with your local details. The TOML file is self documented:
CSV file content¶
The CSV file must start with the mandatory first line with column headers:
The next lines must contain the following columns:
- site, as defined in TOML site section
- id_universal of the sighting to be modified
- path to the attribute to modify, in
JSONPath syntax <https://goessner.net/articles/JsonPath/>_, 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;
Run application¶
The application runs as:
Reference¶
Usage: update_vn [OPTIONS] COMMAND [ARGS]...
Update biolovision database.
CONFIG: configuration filename
INPUT: CSV file listing modifications to be applied
Options:
--verbose / --quiet Increase or decrease output verbosity
--version Show the version and exit.
--help Show this message and exit.
Commands:
init Copy template TOML file to home directory.
update Update Biolovision database.
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: