FAO SMTA API post submiter
Intended use for Gene banks, (*1)
Easysmta is a http post utillity program to register your institute's SMTAs (Standard Material Transfer Agreements). To make it work, you need to have the following:, (*2)
- An account at FAO's Planttreaty site.
- Two database tables or dataviews with SMTA and SMTA material data.
- Make the configuration in this application's config file.
- run bin/easysmta post command. The command uses parameters to limit which SMTAs you are intended to post/register.
Installation
In order to install this library via composer run the following command in the console:, (*3)
composer require endlessdreams/easy-smta-toolkit
or add the package manually to your composer.json file in the require section:, (*4)
"endlessdreams/easy-smta-toolkit": "^1.0"
or globally:, (*5)
composer global require endlessdreams/easy-smta-toolkit
This will install easysmta into the ~/.composer/vendor/ directory and, most importantly, the easysmta CLI tool are installed into ~/.composer/vendor/bin/., (*6)
Simply add this directory to your PATH in your ~/.bash_profile (or ~/.bashrc) like this:, (*7)
export PATH=~/.composer/vendor/bin:$PATH
and easysmta is now available on your command line., (*8)
To keep your tools up to date, you simply do this:, (*9)
composer global update
composer global install
To remove a package, you edit ~/.composer/composer.json and then run composer global update., (*10)
Configuration
Configuration file is located in easysmta application folder: config/local.php.
In this file you will see the following structure:, (*11)
return [
'database' => [
'driver' => getenv('EASYSMTA_DRIVER'),
'database' => getenv('EASYSMTA_DATABASE'),
'username' => getenv('EASYSMTA_USERNAME'),
'password' => getenv('EASYSMTA_PASSWORD'),
'hostname' => getenv('EASYSMTA_HOSTNAME'),
],
'map' => [
'table_order' => 'easysmta',
'table_item' => 'easysmtaitem',
'columns_order' => [
'id' => 'id',
'symbole' => 'symbole',
'date' => 'date',
'type' => 'type',
'language' => 'language',
'shipName' => 'shipname',
'recipient_type' => 'recipient_type',
'recipient_pid' => 'recipient_pid',
'recipient_name' => 'recipient_name',
'recipient_address' => 'recipient_address',
'recipient_country' => 'recipient_country',
'document_location' => 'document_location',
'document_retInfo' => 'document_retinfo'
],
'columns_item' => [
'crop' => 'crop',
'sampleid' => 'sampleid',
'pud' => 'pud',
'ancestry' => 'ancestry'
],
],
'provider' => [
'type' => 'or',
'pid' => getenv('PROVIDER_INSTITUTE_CODE') ?? 'YOUR INSTITUTE CODE',
'name' => getenv('PROVIDER_INSTITUTE_NAME') ?? 'YOUR INSTITUTE NAME',
'address' => getenv('PROVIDER_INSTITUTE_ADDRESS') ?? 'YOUR INSTITUTE ADDRESS',
'country' => getenv('PROVIDER_INSTITUTE_COUNTRY_CODE') ?? 'XXX',
'email' => getenv('PROVIDER_INSTITUTE_EMAIL') ?? 'contact@any.institute'
],
'fao' => [
'username' => getenv('EASYSMTA_FAO_USERNAME'),
'password' => getenv('EASYSMTA_FAO_PASSWORD'),
],
];
To set database and FAO HTTPS API credentials in the config file or exporting environment variables in ~/.bash_profile (or ~/.bashrc)., (*12)
Usage
The examples are written as if your working directory is bin or the application is globally installed., (*13)
To test generate xml to terminal., (*14)
easysmta xml-dry-run
To test generate all smta xml to 2018-01-01. (No https credentials needed here, only to your database), (*15)
easysmta xml-dry-run --to=2018-01-01
To test post all SMTA's until 2018-01-01., (*16)
easysmta register --to=2018-01-01 -t
To test post all SMTA's from 2017-01-01 until 2018-01-01., (*17)
easysmta register --from=2017-01-01 --to=2018-01-01 -t
To actual post all SMTA's until 2018-01-01. (No testing), (*18)
easysmta register --to=2018-01-01
Credits
ir. R (Roel) Hoekstra and dr.ir. TJL (Theo) van Hintum
at Centrum voor Genetische Bronnen Nederland
for letting me look at their dos cmd toolkit., (*19)
Mr Marco Marsella at FAO, Climate, Biodiversity, Land and Water Department, IT for great support., (*20)
Wallogit.com
