OpenSILEX PHIS

https://opensilex.github.io/docs-community-dev/
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### Launch Netbeans

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Start Netbeans by executing the 'netbeans' script located in the installation's bin directory.

```bash
./bin/netbeans

```

--------------------------------

### Install Composer using PHP Script

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Installs Composer globally using the official setup script with specified installation directory and filename.

```bash
php composer-setup.php --install-dir=bin --filename=composer
```

--------------------------------

### Run Netbeans Installer

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Execute the Netbeans installer script to begin the installation process.

```bash
sh ~/Downloads/netbeans-X.X-linux.sh

```

--------------------------------

### Configuration Properties Example

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Example of configuration properties for MongoDB, PostgreSQL, RDF4J, and Webservice.

```properties
# MongoDB configuration
mongo.host=127.0.0.1
mongo.port=27017
mongo.db=<experimental_installation_name>
mongo.user=opensilex
mongo.password=azerty
mongo.authdb=opensilex

# PostgreSQL configuration
pg.host=127.0.0.1
pg.port=5432
pg.db=<experimental_installation_name>
pg.user=opensilex
pg.password=azerty

# RDF4J Configuration
rdf.host=127.0.0.1
rdf.port=8080
rdf.path=rdf4j-server
rdf.infra=opensilex
rdf.repo=opensilex

# Webservice configuration
ws.log.dir=/home/tomcat/apache-tomcat/logs/opensilex-ws

ws.host=127.0.0.1
ws.port=8080
ws.target=phis2ws
ws.baseUrl=rest

ws.doc.host=127.0.0.1
ws.doc.port=8080
ws.doc.name=phis2ws

ws.updir.host=127.0.0.1
ws.updir.user=<Linux session name>
ws.updir.password=<Linux session password>
ws.updir.doc=~/opensilex/documents/instance

ws.images.dir=/var/www/html/images
ws.images.url=http://127.0.0.1/images

ws.layers.dir=/var/www/html/layers
ws.layers.url=http://127.0.0.1/layers

```

--------------------------------

### Enable and Start mongod Service

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Enable the mongod service to start automatically on boot and then start the service.

```bash
sudo systemctl enable mongod
sudo systemctl start mongod
```

--------------------------------

### Install Git

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Installs Git package using apt-get. Git is necessary for cloning repositories.

```bash
sudo apt-get install git

```

--------------------------------

### Install PHP and Extensions

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Install PHP version 7.0 along with the mbstring and dom extensions required for OpenSILEX.

```bash
sudo apt-get update
sudo apt-get install php php-mbstring php-dom

```

--------------------------------

### Create JDK Installation Directory

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Create a directory to store the Java Development Kit (JDK) installation files.

```bash
mkdir ~/jdk

```

--------------------------------

### Install Composer

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Installs Composer using the official installer script. Ensure Curl is installed beforehand.

```bash
sudo curl -sS https://getcomposer.org/installer | sudo php -- --install-dir=/usr/local/bin --filename=composer

```

--------------------------------

### Start Tomcat Service

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Start the Apache Tomcat service using the startup script.

```bash
/home/tomcat/apache-tomcat/bin/startup.sh

```

--------------------------------

### Install Apache2 and PHP Module

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Install the Apache2 web server and the PHP 7.0 module for Apache.

```bash
sudo apt-get update
sudo apt-get install apache2 libapache2-mod-php7.0

```

--------------------------------

### Create Tomcat Installation Directory

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Create a directory in the home folder to store the Apache Tomcat installation files.

```bash
sudo mkdir /home/tomcat

```

--------------------------------

### Start Servers and Check Ports

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Starts Apache2, PostgreSQL, and Tomcat services, then uses nmap to check if their default ports are open.

```bash
sudo systemctl start apache2
sudo systemctl start postgresql
/home/tomcat/apache-tomcat/bin/startup
nmap 127.0.0.1

```

--------------------------------

### Install Git on Linux

Source: https://opensilex.github.io/docs-community-dev/github.html

Installs the Git version control system on a Linux distribution using apt-get. Super-user privileges may be required.

```bash
apt-get install git

```

--------------------------------

### Install PostgreSQL and PostGIS

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Install PostgreSQL and the PostGIS extension on your system using apt-get. These are essential for geospatial data handling in OpenSILEX PHIS.

```bash
sudo apt-get update
 sudo apt-get install postgresql
 sudo apt-get install postgresql-9.5-postgis-2.2
```

--------------------------------

### Run Robo 3T Installation Program

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Execute the Robo 3T program. Replace `<version>` with the specific version number.

```bash
./robo3t<version>  /bin/robo3t
```

--------------------------------

### Install Missing PHP Package

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Installs a missing PHP package identified by Composer.

```bash
sudo apt-get install php-<name of the package given by composer>
```

--------------------------------

### Install Composer Asset Plugin

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Installs the Composer asset plugin globally, which is required for managing frontend assets with Composer.

```bash
sudo composer global require "fxp/composer-asset-plugin:^1.2.0"

```

--------------------------------

### MongoDB Connection Output Example

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

This is an example of the output you should see when successfully connecting to a MongoDB 4.0 instance using the mongo shell. It confirms the server version and connection details.

```text
MongoDB shell version v4.0.4
connecting to: mongodb://127.0.0.1:27017
Implicit session: session { "id" : UUID("bca506e0-589d-482d-a8f2-6da60e56b80c") }
MongoDB server version: 4.0.4
Server has startup warnings:
2018-12-10T12:28:02.828+0100 I STORAGE  [initandlisten] 
2018-12-10T12:28:02.828+0100 I STORAGE  [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2018-12-10T12:28:02.828+0100 I STORAGE  [initandlisten] **          See http://dochub.mongodb.org/core/prodnotes-filesystem
2018-12-10T12:28:03.489+0100 I CONTROL  [initandlisten] 
2018-12-10T12:28:03.489+0100 I CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database. 
2018-12-10T12:28:03.489+0100 I CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2018-12-10T12:28:03.489+0100 I CONTROL  [initandlisten] 
---
```

--------------------------------

### Run MongoDB

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Starts the MongoDB server using its configuration file. This is required for the database operations.

```bash
sudo mongod --config /etc/mongod.conf

```

--------------------------------

### Check Git Version and Help

Source: https://opensilex.github.io/docs-community-dev/github.html

Displays the installed Git version and opens the Git help documentation in the terminal. These commands are also usable on Windows via Git Bash.

```bash
git --version

```

```bash
git --help

```

--------------------------------

### Initialize Replica Set

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Initiate the replica set configuration from the MongoDB shell. This command starts the replica set process.

```javascript
> rs.initiate()
```

--------------------------------

### Function Documentation

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Standard Javadoc format for function documentation, including purpose, error handling, examples, and parameters. Comments generally start with a verb in the third person.

```Java
/**
  * Generates a new vector URI. A vector URI follows this pattern:
  * <prefix>:<year>/<unic_code> 
  * <unic_code> = 1 letter type + 2 numbers year + auto incremented number
  * with 3 digits (per year).
  * Functions comment generally starts with a verb in the third person.
  * @error the error message possible or what happends if an error occured.
  * @example http://www.phenome-fppn.fr/diaphen/2017/v1702
  * @example
  * SELECT ?uri
  * WHERE {
  *     ?uri rdf:type <http://www.phenome-fppn.fr/vocabulary/2017#Vector>   
  * }
  * @param year the insertion year of the vector.
  * @return the new vector URI.
  */
  public String generateVectorUri(String year) {
    ...
  }


```

--------------------------------

### Create PostgreSQL Database

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Creates a new PostgreSQL database, recommended to be named after the experimental installation. The 'opensilex' user is set as the owner.

```sql
CREATE DATABASE <experimental_installation_name> OWNER opensilex;

```

--------------------------------

### Update Apt and Install MongoDB 4.0

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Update the package list to include the new repository and then install the MongoDB 4.0 package.

```bash
sudo apt-get update
sudo apt-get install mongodb-org
```

--------------------------------

### Get Git Remote Help

Source: https://opensilex.github.io/docs-community-dev/github.html

Displays the help documentation for Git remote commands directly in the shell.

```bash
git remote --help
```

--------------------------------

### Check PHP Version

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Verify the installed PHP version from the terminal.

```bash
php --version

```

--------------------------------

### Run MongoDB Service

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Start the MongoDB service using its configuration file. This command ensures MongoDB is running with the specified settings.

```bash
sudo mongod --config /etc/mongod.conf
```

--------------------------------

### Locate PostgreSQL Client

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Find the path to the PostgreSQL client executable (`psql`). This is useful for verifying the installation and connecting to the database.

```bash
which psql
```

--------------------------------

### Start Tomcat Manager App

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Access the Tomcat Manager App to manage deployed applications. Ensure you have the correct Tomcat user credentials.

```bash
sudo -i -u postgres

```

--------------------------------

### Check Java Development Kit Version

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Verify if Java Development Kit (JDK) is installed and check its version from the terminal.

```bash
java -version

```

--------------------------------

### Extract JDK Archive

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Extract the downloaded JDK archive into the specified installation directory.

```bash
tar -xvf ~/Downloads/jdk-X.X.X_linux-x64_bin.tar.gz ~/jdk/

```

--------------------------------

### Create PHIS Alias

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Creates a shell alias to easily start the OpenSILEX PHIS application and open it in the web browser.

```bash
alias phis='apache-tomcat/bin/startup.sh;xdg-open http://localhost/phis-webapp/web'
```

--------------------------------

### MongoDB Web Service Configuration

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Configuration properties for connecting to a MongoDB instance. Ensure the host, port, and database name match your MongoDB setup.

```properties
mongo.host=localhost
mongo.port=27017
mongo.db=opensilex
```

--------------------------------

### Checkout and Pull Latest Changes

Source: https://opensilex.github.io/docs-community-dev/github.html

Before starting work, ensure your local repository is up-to-date by checking out the master branch and pulling the latest changes from the upstream repository.

```bash
git checkout and git pull upstream master
```

--------------------------------

### Extract Robo 3T Archive

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Unpack the downloaded Robo 3T archive. Replace `<version>` with the specific version number and `<Robo 3T repository location>` with your desired installation path.

```bash
tar -xvf ~/Downloads/robo3t<version>  .tar.gz <Robo 3T repository location>
```

--------------------------------

### Extract Tomcat Archive

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Extract the downloaded Apache Tomcat archive into the specified installation directory.

```bash
cd /home/tomcat/
tar --owner=<user> -xvzf ~/Downloads/apache-tomcat<version>.tar.gz

```

--------------------------------

### Update Composer Dependencies

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Runs the Composer update command to install or update project dependencies, ignoring platform requirements.

```bash
composer update --ignore-platform-reqs
```

--------------------------------

### Java Bean Validation Example

Source: https://opensilex.github.io/docs-community-dev/webService

Demonstrates using JSR 380 annotations for input validation in a Java web service. Includes validation for query parameters and complex object lists.

```java
public class ExampleResourceService {

  @GET
  public Response get(
    @QueryParam("url") @Required @URL String url
  ) {
    ...
  }

  @POST
  public Response post(ArrayList<ExampleDTO> @Valid examples) {
    ...
  }
}

public class ExampleDTO {
  String url;
  SecondExample secondExample;

  @URL
  @Required
  public String getUrl() {
    return url;
  }

  @Valid
  public SecondExample getSecondExample() {
    return secondExample;
  }
}

```

--------------------------------

### Check MongoDB Version

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Use this command to verify your installed MongoDB version. This is crucial for ensuring compatibility with OpenSILEX PHIS v3.0, which requires at least MongoDB v4.0.

```bash
mongod --version
```

--------------------------------

### Create Project Directory

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Creates a directory named 'OpenSILEX' in the user's home directory to store project files.

```bash
mkdir ~/OpenSILEX

```

--------------------------------

### Register MongoDB 4.0 GPG Key

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Add the public GPG key for MongoDB 4.0 to your system's trusted keys. This is necessary for verifying the authenticity of the MongoDB packages during installation.

```bash
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
```

--------------------------------

### Acquisition Session Metadata JSON Structure

Source: https://opensilex.github.io/docs-community-dev/4p

This JSON structure represents the data retrieved from the `GET /acquisitionSessions/metadataFile` webservice. It includes pagination details, status, data files, and the actual metadata for acquisition sessions, with each object in the 'data' array corresponding to a row in an Excel sheet.

```json
{
  "metadata": {
    "pagination": {
      "pageSize": 20,
      "currentPage": 0,
      "totalCount": 24,
      "totalPages": 2
    },
    "status": [],
    "datafiles": []
  },
  "result": {
    "data": [
      {
        "Camera_type": null,
        "Camera_alias": null,
        "Camera_uri": null,
        "Vector_type": "http://www.phenome-fppn.fr/vocabulary/2017#UAV",
        "Vector_alias": "my-drone",
        "Vector_uri": "http://www.phenome-fppn.fr/my-installation/2018/v1802",
        "RadiometricTarget_uri": null,
        "RadiometricTarget_alias": null,
        "Installation": "http://www.phenome-fppn.fr/my-installation",
        "GroupPlot_type": "http://www.phenome-fppn.fr/vocabulary/2017#Experiment",
        "GroupPlot_alias": "EX_18",
        "GroupPlot_uri": "http://www.phenome-fppn.fr/my-installation/EXP2018-1",
        "GroupPlot_species": "maize, appletree",
        "Pilot": "uav.pilot@example.com"
      },
      {"..."}
    ]
  }
}
```

--------------------------------

### Create PostgreSQL Database and Extension

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

SQL commands to create the OpenSILEX database and enable the PostGIS extension. Ensure you have the necessary privileges.

```sql
CREATE DATABASE opensilex OWNER opensilex;
CREATE EXTENSION postgis;
select postgis_full_version();
\q
```

--------------------------------

### Create Web Service Directories

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Creates necessary directories for OpenSILEX web service, including instance documents, images, and layers. It also sets ownership and permissions for these directories.

```bash
mkdir -p ~/opensilex-ws/documents/instance
sudo mkdir /var/www/html/images
sudo mkdir /var/www/html/layers
sudo chown -R <user>:<user> /var/www/html/images
sudo chown -R <user>:<user> /var/www/html/layers
sudo chown -R <user>:<user> ~/opensilex-ws/documents/
sudo chmod -R 775 /var/www/html/images
sudo chmod -R 775 /var/www/html/layers
sudo chmod -R 775 ~/opensilex-ws/documents/

```

--------------------------------

### Configure Application Name and Hostname

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Set the application name and hostname, which determine the URL at which the application is accessible.

```php
# Application name, accessible at the URL http://$hostname/$appli
$appli = 'opensilex';
$hostname = 'localhost';
```

--------------------------------

### Configure OpenSILEX Web Service Paths

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Define the base paths for OpenSILEX web services, including the REST API and documentation.

```php
//	http://{ws.host}:{ws.port}/{ws.target}/{ws.baseUrl}/
define('WS_PHIS_PATH',	'http://localhost:8080/opensilex/rest/');
//	http://{ws.host}:{ws.port}/{ws.name}
define('WS_PHIS_PATH_DOC',	'http://localhost:8080/opensilex');
```

--------------------------------

### Build with Maven Profile

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Command to build the project using a specific Maven profile (e.g., 'test').

```bash
mvn install -Ptest

```

--------------------------------

### Enable PostGIS Extension

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Connects to the specified PostgreSQL database as the 'opensilex' user and enables the PostGIS extension, which provides geospatial capabilities. It also displays the PostGIS version.

```bash
psql -U opensilex -h 127.0.0.1 -d <experimental_installation_name>

```

```sql
CREATE EXTENSION postgis;
select postgis_full_version();

```

--------------------------------

### List Git Configuration

Source: https://opensilex.github.io/docs-community-dev/github.html

Displays the current Git configuration settings. This command helps verify that the user's email and name have been set correctly.

```bash
git config --list

```

--------------------------------

### Configure Web Services Path

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Sets the necessary paths for the web services in the configuration file.

```php
define('WS_PHIS_PATH', 'http://localhost:8080/phis2ws/rest/');
define('WS_PHIS_PATH_DOC', 'http://localhost:8080/phis2ws');
```

--------------------------------

### Check MongoDB Access with User Credentials

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

Verify access to the 'mydatabase' by connecting using the 'opensilex' user and 'azerty' password, specifying the authentication database.

```shell
mongo -u "opensilex" -p "azerty" --authenticationDatabase "mydatabase" "mydatabase"
```

--------------------------------

### Set Platform Configuration

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Configure the platform identifier for the OpenSILEX application.

```php
'platform' => 'Demo'
```

--------------------------------

### Navigate to Web Application Directory

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Changes the current directory to the web application's root folder.

```bash
cd /var/www/html/phis-webapp
```

--------------------------------

### OpenSILEX Web Service General Configurations

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

General configuration settings for the OpenSILEX web service, including logging directory, host, port, and file upload settings.

```properties
#	Logs	 repertory.	 You	 need	 to	 create	 this	 directory
#	(do	 not	 forget	 the	 access	 rights!)
ws.log.dir=/home/training/opensilex/logs
#	The	 web	 service	 url	 access	 will	 be:
#	http://{ws.host}:{ws.port}/{ws.target}/{ws.baseUrl}
ws.host=localhost
ws.port=8080
#	Name	 of	 the	 application	 - 	 can	 be	 personalized	 in	 the	 pom.xml	 file
ws.target=opensilex
ws.baseUrl=rest
ws.doc.host=localhost
ws.doc.port=8080
ws.doc.name=opensilex
ws.pageSize.max=2097152
ws.updir.host=opensilex
ws.updir.user=username
ws.updir.password=password
#	Files	 storage	 directory	 (do	 not	 forget	 the	 access	 rights)
ws.updir.doc=/home/training/opensilex/documents/{rdf.infra}
```

--------------------------------

### Download OpenSILEX Webapp Release

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Use this command to download a specific release of the OpenSILEX web application from GitHub.

```bash
git clone --branch 3.2.4 https://github.com/OpenSILEX/phis-webapp.git
```

--------------------------------

### Run Netbeans IDE

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Command to launch the Netbeans IDE from the terminal.

```bash
~/netbeans/bin/netbeans

```

--------------------------------

### Set Web Application File Permissions

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Commands to set ownership and permissions for the OpenSILEX web application files. Ensure the user and group match your Apache configuration.

```bash
sudo chown -R <username>:www-data /var/html/phis-webapp
sudo chmod -R 775 /var/html/phis-webapp

```

--------------------------------

### Remove Older MongoDB Version and Data

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Purge existing MongoDB packages and remove the old data directory. This ensures a clean slate for the new installation. The data directory is then recreated and ownership is set.

```bash
sudo apt-get purge mongodb-org*
sudo rm -rf /var/lib/mongodb
sudo mkdir /var/lib/mongodb/
sudo chown -R mongodb:mongodb /var/lib/mongodb/
```

--------------------------------

### Clone Repository using HTTPS

Source: https://opensilex.github.io/docs-community-dev/github.html

Use this command to create a local copy of your GitHub repository using the HTTPS protocol. This is an alternative to SSH but may require repeated authentication.

```bash
git clone <copied HTTPS URL>
```

--------------------------------

### Create PostgreSQL User

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Creates a new PostgreSQL user named 'opensilex' with elevated privileges, including the ability to create databases and superuser status. Sets an encrypted password for the user.

```bash
psql

```

```sql
CREATE USER opensilex;
ALTER ROLE opensilex WITH CREATEDB;
ALTER ROLE opensilex WITH SUPERUSER;
ALTER USER opensilex WITH ENCRYPTED PASSWORD 'azerty';

```

--------------------------------

### Create Admin User for OpenSILEX Database

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

Create a new user with 'readWrite' role for the 'opensilex' database. This allows the user to manage collections and data within that specific database.

```javascript
db.createUser(
 {
   user: "opensilex",
   pwd: "azerty",
   roles: [ { role: "readWrite", db: "opensilex" } ]
 }
)
```

--------------------------------

### Run Robo 3T

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Launches the Robo 3T GUI client for MongoDB. This tool is used to manage MongoDB connections and databases.

```bash
~/robo3t/bin/robo3t

```

--------------------------------

### Create and Checkout a New Branch

Source: https://opensilex.github.io/docs-community-dev/github.html

Creates a new branch and immediately switches to it, preparing it for development. The command `git branch <new_branch_name>` is preferred for just creating a branch.

```bash
git checkout -b <new_branch_name>
```

--------------------------------

### Clone Ontology Vocabularies

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Clones the ontology-vocabularies repository from GitHub into the ~/OpenSILEX directory. Consider cloning a specific release tag for stability.

```bash
cd ~/OpenSILEX
git clone https://github.com/OpenSILEX/ontology-vocabularies.git

```

--------------------------------

### Interface and Class Structure with Blank Lines

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Demonstrates the correct usage of blank lines between interface and class definitions, and within class members. Two blank lines separate sections, one blank line separates methods and local variables.

```Java
/**
 * Comment.
 */
public interface MyInterface {
    Boolean isEmptyMethod();
}


/**
 * Comment.
 */
class Sample extends Object {
    int ivar1;
    int ivar2;

    Sample(int i, int j) {
        int k;

        i = k;

        /* Comment. */
        ivar1 = i;
        ivar2 = j;     
    }

    int emptyMethod() {}

    Boolean isEmptyMethod() {}
    ...
}


```

--------------------------------

### Connect to MongoDB Shell

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Attempt to connect to the MongoDB instance using the mongo shell to verify the upgrade and service status. The output shows the shell version, server version, and startup warnings.

```bash
mongo
```

--------------------------------

### Clone Repository using SSH

Source: https://opensilex.github.io/docs-community-dev/github.html

Use this command to create a local copy of your GitHub repository using the SSH protocol. Ensure your SSH connection is configured.

```bash
git clone <copied SSH URL>
```

--------------------------------

### PostgreSQL Web Service Configuration

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Configuration properties for connecting to a PostgreSQL database. Update the host, port, database name, username, and password as needed.

```properties
pg.host=localhost
pg.port=5432
pg.db=opensilex
pg.user=username
pg.password=password
```

--------------------------------

### Configure Replica Set Name

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Add this configuration to your mongod.conf file to specify the replica set name. Replace 'opensilex' with your desired name.

```yaml
replication:
  replSetName: "opensilex"
```

--------------------------------

### Configure Git User Email and Name

Source: https://opensilex.github.io/docs-community-dev/github.html

Sets the global Git configuration for the user's email and name, which will appear in the Git log. This configuration is done once per system.

```bash
git config --global user.email "<the email you use on GitHub>"
git config --global user.name "<the name that will appear on the git log>"

```

--------------------------------

### OpenSILEX Web Service Configuration Properties

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Configuration properties for the OpenSILEX web service, including logging, host, port, and file server settings. Ensure these paths and ports are correctly set for your environment.

```properties
[...]
logDirectory=/home/tomcat/phis2ws/logs

[...] host=127.0.0.1:8080
basePath=/phisws/rest
[...]
webAppHost=127.0.0.1
webAppPort=8080
[...]
webAppApiDocsName=phis2ws
[...]
webAppApiBasePath=/phis2ws/resources

[...]
uploadFileServerPort=22
# Adresse de sauvegarde des donn
uploadFileServerIP=127.0.0.1
uploadFileServerUsername=<linux session username>
uploadFileServerPassword=<linux session password>
uploadFileServerDirectory=/home/<user>/phis-ws/documents/instance
uploadImageServerDirectory=/var/www/html/images
layerFileServerDirectory=/var/www/html/layers
layerFileServerAddress=http://127.0.0.1/layers
[...]


```

--------------------------------

### Import PostgreSQL Dump

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Command to import a SQL dump file into the PostgreSQL database. Replace the path with the actual location of your dump file.

```bash
psql -U opensilex opensilex < Documents/opensilex_st_dump.sql
```

--------------------------------

### Configure PostgreSQL Listen Addresses

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Edits the postgresql.conf file to allow connections from any IP address.

```ini
listen_addresses: '*'
```

--------------------------------

### Experiment Form Styling

Source: https://opensilex.github.io/docs-community-dev/webapp

Specifies the Bootstrap class .well for styling new forms, as shown in the experiment form.

```php
<div class="experiment-form well">

   <?php $form = ActiveForm::begin(); ?>

```

--------------------------------

### Dump MongoDB Database

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Use this command to create a backup of your MongoDB database before performing an upgrade. It saves all data into a dump folder in the current directory.

```bash
mongodump --host localhost
```

--------------------------------

### Commit Changes with a Message

Source: https://opensilex.github.io/docs-community-dev/github.html

Use this command to record staged changes to the local repository with a descriptive message. The message should concisely explain the nature of the changes.

```bash
git commit -m <short and informative message>

```

--------------------------------

### Clone OpenSILEX PHIS Web Service

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Clones the phis-ws repository from GitHub into the ~/OpenSILEX directory. Consider cloning a specific release tag for stability.

```bash
cd ~/OpenSILEX
git clone https://github.com/OpenSILEX/phis-ws.git

```

--------------------------------

### Clone OpenSILEX Web Service Repository

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Download the latest release of the OpenSILEX web service (phis-ws) using Git. This command clones the specific branch for version 3.2.4.

```bash
git clone --branch 3.2.4 https://github.com/OpenSILEX/phis-ws.git
```

--------------------------------

### Class Documentation

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Standard Javadoc format for class documentation, including purpose, author, update history, and parameter types. Comments begin with a capital letter and end with a dot.

```Java
/**
 * DAO mother class.
 * Provides generic functions to query the storage.
 * Comments begins with a capital letter and ends with a dot.
 * The @author tag designates the main contributors of the class. A contributor that
 * updates the class won't be considered as an @author. The case of a reworked class will be discussed.
 * @update [Arnaud Charleroy] 4 Sept. 2018: explanation.
 * @update [Morgane Vidal, Andréas Garcia] 18 Sept. 2018: explanation.
 * @see optional link to class or website that helps the comprehension of the class.
 * @param <T> the type of object handled.
 * @author Morgane Vidal <morgane.vidal@inra.fr>, Arnaud Charleroy <arnaud.charleroy@inra.fr>
 */
 public class UriGenerator {

   /**
    * Comment which explains the complexeAttribute purpose.
    * @example possible value for this attribute without parenthesis.
    */
   private String complexeAttribute;

   // Comment which explains the simpleAttribute purpose with an example if needed.
   private String simpleAttribute;
 }


```

--------------------------------

### Navigate to Robo 3T Directory

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Change the current directory to the location where Robo 3T was extracted. This is necessary before running the executable.

```bash
cd <Robo 3T repository location>
```

--------------------------------

### Copy WAR Archive to Tomcat

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Command to copy the generated WAR file to the Tomcat webapps directory.

```bash
cp <phis-ws git repository>/target/phis2ws.war /home/tomcat/apache-tomcat/webapps/phis2ws.war

```

--------------------------------

### Check Netbeans Folder Permissions

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Lists the permissions of files and folders within the Netbeans configuration directory.

```bash
ls -l ~/.netbeans/8.2
```

--------------------------------

### Copy Web Application to Apache Root

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Copies the phis-webapp folder to the Apache web server's root directory.

```bash
sudo cp -r <Git folder>/phis-webapp /var/www/html
```

--------------------------------

### Register New BrAPI Service

Source: https://opensilex.github.io/docs-community-dev/brapiImplementation

Register your new BrAPI service implementation within the application's configuration by binding it to the `BrapiCall.class`. This ensures that your service is recognized and can be injected where needed.

```java
register(new AbstractBinder() {
    @Override
    protected void configure() {
        // create the session from the last sessionId received
        bindFactory(SessionFactory.class).to(Session.class);
        // Session injection thanks to the type defined in SessionInjectResolver
        bind(SessionInjectResolver.class)
                .to(new TypeLiteral<InjectionResolver<SessionInject>>() {
                })
                .in(Singleton.class);
        //Brapi services injection
        bind(CallsResourceService.class).to(BrapiCall.class);
        bind(NewBrapiResourceService.class).to(BrapiCall.class);
    }
});
```

--------------------------------

### List and Manage Git Branches

Source: https://opensilex.github.io/docs-community-dev/github.html

Commands for listing existing branches, creating new ones, switching between them, and deleting them. Deleting a branch requires pushing the deletion to the remote.

```bash
git branch
```

```bash
git branch <new_branch_name>
```

```bash
git checkout <new_branch_name>
```

```bash
git branch -d <branch_name>
```

```bash
git push origin :<branch_name>
```

--------------------------------

### Clone OpenSILEX PHIS Web Application

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Clones the phis-webapp repository from GitHub into the ~/OpenSILEX directory. Consider cloning a specific release tag for stability.

```bash
cd ~/OpenSILEX
git clone https://github.com/OpenSILEX/phis-webapp.git

```

--------------------------------

### Add Upstream Remote Repository

Source: https://opensilex.github.io/docs-community-dev/github.html

Use this command to add the main OpenSILEX repository as an 'upstream' remote. This is recommended for tracking changes from the original project.

```bash
git remote add upstream https://github.com/OpenSILEX/docs-community-dev.git
```

--------------------------------

### Extract RDF4J Archive

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Extract the downloaded RDF4J SDK archive to the home directory.

```bash
unzip ~/Downloads/eclipse-rdf4j-<version>-sdk.zip -d ~/

```

--------------------------------

### Configure MongoDB Storage Path

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Modify the MongoDB configuration file to specify the database storage path. Ensure the MongoDB user has ownership of this directory.

```bash
sudo chown -R mongodb:mongodb <dbPath>
```

--------------------------------

### Implement BrAPI Call Information

Source: https://opensilex.github.io/docs-community-dev/brapiImplementation

Implement the `BrapiCall` interface to override the `callInfo()` method. This method provides essential details about your new BrAPI call, including its name, supported data types, HTTP methods, and versions.

```java
public class CallsResourceService implements BrapiCall {
    final static Logger LOGGER = LoggerFactory.getLogger(CallsResourceService.class);
    /** 
     * Overriding BrapiCall method
     * @date 27 Aug 2018
     * @return Calls call information */
    @Override
    public Call callInfo() {
        ArrayList calldatatypes = new ArrayList<>();
        calldatatypes.add("json");
        ArrayList callMethods = new ArrayList<>();
        callMethods.add("GET");
        ArrayList callVersions = new ArrayList<>();
        callVersions.add("1.1");
        callVersions.add("1.2");
        Call callscall = new Call("calls", calldatatypes, callMethods, callVersions);
        return callscall;
    }
}
```

--------------------------------

### RDF4J Web Service Configuration

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Configuration settings for the RDF4J triple store. This includes base URI, host, port, repository ID, and vocabulary context.

```properties
#	Base	 of	 the	 generated	 URIs	 - 	 can	 be	 personalized:
rdf.base.uri=http://www.opensilex.org/
#	RDF4J	 localisation	 and	 repository	 ID:
rdf.host=localhost
rdf.port=8080
rdf.path=rdf4j-server
rdf.repo=opensilex
#	Managed	 infrastructure	 - 	 can	 be	 personalized:rdf.infra=opensilex
#	3	 letters	 code	 for	 the	 infrastructure:
rdf.infra.code=OSX
#	Context	 of	 the	 vocabulary.	 Oeso	 by	 default:
rdf.vocabulary.context=http://www.opensilex.org/vocabulary/oeso
```

--------------------------------

### Copy RDF4J WAR files to Tomcat

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Copy the RDF4J web application archive (.war) files to the Tomcat webapps directory.

```bash
cp ~/eclipse-rdf4j-<version>/war/* /home/tomcat/apache-tomcat/webapps/

```

--------------------------------

### Set Folder Permissions for Web Application

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Changes ownership and permissions for the phis-webapp directory to ensure proper access for the web server and user.

```bash
sudo chown -R <username>:www-data /var/www/html/phis-webapp
sudo chmod 775 -R /var/www/html/phis-webapp
```

--------------------------------

### Test SSH Connection to GitHub

Source: https://opensilex.github.io/docs-community-dev/github.html

Tests the SSH connection to GitHub to ensure successful authentication. A success message indicates that the SSH key is correctly configured.

```bash
ssh -T git@github.com

```

--------------------------------

### Configure MongoDB for Remote Connections

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

Comment out network interface configuration lines in `/etc/mongod.conf` to allow remote connections. This includes disabling the default `bindIp` setting.

```properties
# network interfaces
net:
 port: 27017
 bindIp: 127.0.0.1
```

--------------------------------

### Restore MongoDB Database

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Use this command to restore your MongoDB database from the dump created earlier. Run this in the same directory where the `mongodump` command was executed.

```bash
mongorestore --host localhost
```

--------------------------------

### Keyword Spacing with Parentheses

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Illustrates correct spacing around keywords followed by parentheses. A space is required between the keyword and the opening parenthesis, with no space after the closing parenthesis and before the opening curly brace.

```Java
if (expression) {
}

for (expression) {
}

while (expression) {
}


```

--------------------------------

### Add and Commit Local Modifications

Source: https://opensilex.github.io/docs-community-dev/github.html

Stages all changes in the current directory for commit using 'git add' and then commits them to the master branch with a descriptive message using 'git commit'.

```bash
git add .
git commit -m "Your commit message"

```

--------------------------------

### Restart PostgreSQL Service

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Apply changes made to the PostgreSQL configuration by restarting the service. This ensures the new port or settings are active.

```bash
sudo systemctl restart postgresql
```

--------------------------------

### Configure Apache2 Port

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Edit the ports.conf file to change the listening port for Apache2 to 80.

```bash
sudo nano /etc/apache2/ports.conf

```

--------------------------------

### Boolean Function Return Documentation

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Specific Javadoc format for documenting boolean return values, explaining both true and false conditions. Used when a function returns a boolean.

```Java
/**
  * @return true explanation
  *         false explanation
  */


```

--------------------------------

### Set Webapp Files Group for Apache Access

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Change the group ownership of the webapp files to allow the Apache web server to read them.

```bash
chown -R training:www-data /home/training/opensilex/phis-webapp
```

--------------------------------

### Restart Apache2 Service

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Restart the Apache2 service to apply the configuration changes.

```bash
sudo systemctl restart apache2

```

--------------------------------

### SILEX To-Do Tag

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Indicates code that needs to be written, explained in simple terms.

```plaintext
//SILEX:todo
Code to write, explained in simple words.
//\SILEX:todo
```

--------------------------------

### Configure PostgreSQL Peer Authentication

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Modifies the pg_hba.conf file to change authentication from peer to md5 for local connections.

```sql
local all all peer
```

```sql
local all all md5
```

--------------------------------

### Configure PostgreSQL Host Authentication

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Modifies the pg_hba.conf file to allow connections from a specific IP address using MD5 authentication.

```sql
hosts all all <ipaddress> md5
```

--------------------------------

### Edit MongoDB Configuration File

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

Opens the MongoDB configuration file using 'gedit' with super-user privileges. This command allows modification of settings like the replica set name.

```bash
sudo gedit /etc/mongod.conf
```

--------------------------------

### Test MongoDB Authentication

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

Use this command to test authentication by connecting to the 'admin' database and authenticating with provided credentials.

```javascript
use admin
db.auth("superadmin", "mydatabase")
```

--------------------------------

### Configure PostgreSQL Port

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Edit the `postgresql.conf` file to change the default port for the PostgreSQL service. Ensure the new port is not in use.

```bash
nano /etc/postgresql/9.5/main/postgresql.conf
```

--------------------------------

### Enable MongoDB Fork Mode

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Add `fork: true` to the MongoDB configuration file to ensure it runs as a daemon. This is recommended for stable operation.

```ini
# how the process runs
processManagement:*
  fork: true
```

--------------------------------

### Restart PostgreSQL Service

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Command to restart the PostgreSQL database service. Use this if you suspect database connectivity issues.

```bash
sudo systemctl restart postgresql

```

--------------------------------

### Grant Read/Write Permissions for Netbeans Folder

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Grants read and write permissions to the owner and group for Netbeans configuration files and folders.

```bash
sudo chmod -R ug+rw ~/.netbeans
```

--------------------------------

### Generate PostgreSQL Dump

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Generates a PostgreSQL database dump file. Options include excluding owner information (-O) and dumping only the schema (-s). Specify the host and user for the connection.

```bash
# from postres server
pg_dump -O -U opensilex <experimental_installation_name> > opensilex_st_dump.sql
# -O : --no-owner
# -s : only schema
# -h <IP> : postgres host
# -U <user> : user

```

--------------------------------

### Method Call Spacing

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Shows the correct spacing for method calls, emphasizing no space between the method name and its opening parenthesis. This distinguishes method calls from keywords.

```Java
callMethod();
this.myMethod();


```

--------------------------------

### Add MongoDB 4.0 Repository

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Configure your system's package manager to include the MongoDB 4.0 repository. This command is specific to Debian 9 (Stretch). Refer to MongoDB documentation for other distributions.

```bash
echo "deb http://repo.mongodb.org/apt/debian stretch/mongodb-org/4.0 main" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.0.list
```

--------------------------------

### Activate Animated Multiple Background Images

Source: https://opensilex.github.io/docs-community-dev/webapp

Activates the animated multiple background images feature by adding the FullScreenImageSliderWidget to the site index view. Image links are relative to the web/images directory.

```php
use app\components\widgets\FullScreenImageSliderWidget;

      <?= 
         FullScreenImageSliderWidget::widget([
               FullScreenImageSliderWidget::IMAGES_URL_LINK => [ // local image links
                  "background/wallpaper_grapes_vine.jpg",
                  "background/wallpaper_leaf.jpg",
                  "background/wallpaper_tomato.jpg",
                  "background/wallpaper_vine.jpg"
               ],
            // FullScreenImageSliderWidget::DURATION_PER_IMAGE => 10 // time in seconds between two images
         ]);
      ?>
```

--------------------------------

### Binary Operator Spacing

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Illustrates correct spacing for binary operators. Spaces are required between the operator and its operands, except for the dot operator. Unary operators should not be separated from their operands.

```Java
a += c + d;
a = (a + b) / (c * d);


```

--------------------------------

### Variable Assignment Spacing

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Demonstrates the required spacing around the assignment operator (=) for variable assignments. A space is required on both sides of the equals sign.

```Java
myVariable = 33;


```

--------------------------------

### Edit Tomcat Server XML

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Edit the server.xml file to configure the HTTP port for Tomcat.

```bash
nano /home/tomcat/apache-tomcat/conf/server.xml

```

--------------------------------

### Generate MD5 Password

Source: https://opensilex.github.io/docs-community-dev/localInstallation.html

Generates an MD5 hash for a given password string, useful for password management in certain systems.

```bash
 echo -n bonjour | md5sum

```

--------------------------------

### Restart MongoDB Service

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Restart the MongoDB service after updating the configuration file to apply the changes.

```bash
sudo systemctl restart mongod
```

--------------------------------

### Check Replica Set Status

Source: https://opensilex.github.io/docs-community-dev/MongoDBUpgradeTov4

Check the status of the replica set to ensure it has been initialized correctly.

```javascript
> rs.status()
```

--------------------------------

### Create Superadmin User

Source: https://opensilex.github.io/docs-community-dev/MongoDBInstallv4

Creates a new administrative user with privileges to manage users across all databases. This is a fundamental step for enabling authentication and securing your MongoDB instance.

```javascript
use admin
db.createUser(
  {
    user: "useradmin",
    pwd: "pwd",
    roles: [ { role: "userAdminAnyDatabase", db: "admin" } ]
  }
)
```

--------------------------------

### SILEX Login Tag

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Highlights temporary login code blocks used in the PHIS main client.

```plaintext
//SILEX:login
Used in the PHIS main client, to highlight the temporary login blocks of code.
//\SILEX:login
```

--------------------------------

### File Header Comment

Source: https://opensilex.github.io/docs-community-dev/codingStyle

Standard file header comment format including copyright, creation date, and contact information. Used for Java and PHP files.

```Java
//******************************************************************************
//                                ${nameAndExt}
// SILEX-PHIS
// Copyright © INRA ${date?date?string("yyyy")}
// Creation date: ${date}
// Contact: ${userEmail}, anne.tireau@inra.fr, pascal.neveu@inra.fr
//******************************************************************************


```

--------------------------------

### Set Meta Refresh for Web App Redirect

Source: https://opensilex.github.io/docs-community-dev/install-cheatsheet

Configure an automatic redirect to the web application's main interface using a meta refresh tag.

```html
<meta http-equiv="refresh" content="0; URL=http://localhost/phis/web">
```
Tokens:
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