Setting up VLSM on a Windows Machine

0. Download

Notepad++ or MicroSoft VS Code
WampServer from https://www.wampserver.com/en/. Check if Windows is 32 bit or 64 bit. Download WampServer 32 or 64 bit version based on the windows machine
VC Packages

1. Installing WAMP Server

Ensure Windows system is updated. This is important to ensure there is no issue on WampServer later on.
Install VC Packages that we downloaded already - for 64 bit you need to install all, for 32 bit only install 32 bit ones
Reboot machine after installing
Now run WampServer and ensure it is showing green icon

2. Configuring PHP and MySQL

2.1 PHP Setup

Download cacert.pem from https://curl.se/docs/caextract.html. Place it in C:\wamp\ or C:\wamp64\ path. This is needed to allow the application to communicate with VLSTS
Change PHP version to 8.2.13. To do this, click on WampServer -> PHP -> version -> 8.2.13
Next we will change PHP settings to make them more optimum for VLSM. To do this, click on WampServer -> PHP -> php.ini
- When the file opens search for memory_limit. Change 128mb to 2G (or more if there is more RAM available on the computer)
- Now search for post_max_size. Change 8M to 500M
- Now search for upload_max_filesize. Change 2M to 500M
- Find ;openssl.cafile= and change it to openssl.cafile='C:\wamp\cacert.pem' or openssl.cafile='C:\wamp64\cacert.pem'
- Find ;curl.cainfo = and change it to curl.cainfo ='C:\wamp\cacert.pem' or curl.cainfo ='C:\wamp64\cacert.pem'
- Now search for error_reporting. Change it to error_reporting = E_ALL & ~E_NOTICE & ~E_STRICT & ~E_DEPRECATED & ~E_WARNING
- Now search for max_execution_time. Change it to max_execution_time = 1200

Open the php.ini file inside the C:\wamp64\bin\php\php8.2.13\php.ini and do these same edits there as well

2.2 MYSQL Setup

Fixing the MySQL mode
- Click on WampServer icon -> MySQL -> my.ini
- When the file opens, search for sql_mode if it is already set comment out that line by adding a semi-colon ; in the beginning of the line and add the following lines after that:
```
sql_mode =
innodb_strict_mode = 0
```
- Search for innodb_default_row_format=compact and change it to innodb_default_row_format=dynamic
- If it is not there then just add innodb_default_row_format=dynamic
- Close the text file
Next we will change MySQL password.
- WampServer icon -> MySQL -> MySQL Console
- Username is root
- Password is blank (just press enter when it asks for password)
- Now type this:
```
ALTER USER 'root'@'localhost' IDENTIFIED WITH  mysql_native_password BY 'PASSWORD';
FLUSH PRIVILEGES;
exit;
```
- Press enter after pasting these lines in the terminal
Click on Wampserver icon and Restart all services
Download latest version of composer from https://getcomposer.org/download/

3. Setting up VLSM

3.1 VLSM Application Setup

Download VLSM from https://github.com/deforay/vlsm
Unzip and put it in C:\wamp\www\vlsm or C:\wamp64\www\vlsm path
Put the composer.phar also inside the vlsm folder
To complete VLSM installation, open the terminal and run the composer

cd C:\wamp64\www\vlsm

C:\wamp64\bin\php\php8.2.13\php.exe composer.phar updateinstall --no-dev
C:\wamp64\bin\php\php8.2.13\php.exe composer.phar dump-autoload -o

The latest VLSM database is inside the vlsm/sql/init.sql file.
Start phpmyadmin by typing http://localhost/phpmyadmin in browser (login id is root and password is mko)(*&^)
Click on SQL menu on top and type the following line CREATE DATABASE `vlsm` CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci;
This will create a blank vlsm database. Now click on vlsm on left and import the sql file downloaded earlier

Rename the file configs/config.production.dist.php to configs/config.production.php
Enter Database User, Password, DB Name etc.


// VLSTS URL
$systemConfig['remoteURL'] = 'https://STSURL';


// Enable/Disable Modules
// true => Enabled
// false => Disabled
$systemConfig['modules']['vl'] = false;
$systemConfig['modules']['eid'] = true;
$systemConfig['modules']['covid19'] = false;
$systemConfig['modules']['hepatitis'] = false;
$systemConfig['modules']['tb'] = false;

// Database Settings
$systemConfig['database']['host']       = 'localhost';
$systemConfig['database']['username']   = 'root';
$systemConfig['database']['password']   = 'PASSWORD';
$systemConfig['database']['db']         = 'vlsm';
$systemConfig['database']['port']       = 3306;
$systemConfig['database']['charset']    = 'utf8mb4';

.
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// Enable/Disable Interfacing
// true => Enabled
// false => Disabled
$systemConfig['interfacing']['enabled'] = true;

// Interfacing Database Details (not needed if above feature set to false)
$systemConfig['interfacing']['database']['host'] = 'localhost';
$systemConfig['interfacing']['database']['username'] = 'root';
$systemConfig['interfacing']['database']['password'] = 'PASSWORD';
$systemConfig['interfacing']['database']['db'] = 'interfacing';
$systemConfig['interfacing']['database']['port'] = 3306;
$systemConfig['interfacing']['database']['charset'] = 'utf8mb4';

Next step is creating a virtual host pointing to the vlsm application
- Start notepad or notepad++ as admin user (go to start menu, search for notepad and right click and click on Run as administrator)
- open this file C:\windows\system32\drivers\etc\hosts
- Add this line at the bottom 127.0.0.1 vlsm and save & close the file
- Next open C:\wamp\bin\apache\apache2.4.54.2\conf\extra\httpd-vhosts.conf
- change the existing vhost to the following:
```
<VirtualHost *:80>
  ServerName localhost
  ServerAlias vlsm
  DocumentRoot "${INSTALL_DIR}/www/vlsm/public"
  <Directory "${INSTALL_DIR}/www/vlsm/public/">
    AddDefaultCharset UTF-8
    Options +Indexes +Includes +FollowSymLinks +MultiViews
    AllowOverride All
    Require local
  </Directory>
</VirtualHost>
```
- Save & Close this file
- Click on WampServer icon and Restart all services

Now go the command prompt and type these commands:

C:\wamp64\bin\php\php8.2.13\php.execd C:\wamp64\www\vlsm\app\system\migrate.php -yqvlsm

C:\wamp64\bin\php\php8.2.13\php.exe C:\wamp64\www\vlsm\app\scheduled-jobs\remote\commonDataSync.phpcomposer.phar C:\wamp64\bin\php\php8.2.13\php.exe  C:\wamp64\www\vlsm\app\run-once\update-privileges.phppost-install

Now open http://vlsm
- Register a new Admin user and Login
- Fill the instance details in the popup. Select BOTH for type of Instance
- Now scroll to the bottom and click on Force Remote Sync. Please wait for the sync to finish.
Once sync is finished go to http://vlsm/system-admin
- Secret Key can be found in C:\wamp64\www\vlsm\app\system-admin\secretKey.txt
- Register new System Admin and Login
- Select Instance Type as 'Lab Instance' and then select the Lab name from dropdown and click on Submit. (Ignore SMTP settings)
- You can sign out
Users can now start using vlsm from http://vlsm URL

3.2 Task Scheduler

Run Task Scheduler. Click on "Create Task"
Name : VLSM TASK
Select "Run whether user is logged on or not"
Now Go to the ‘Triggers’ tab which is next to the ‘General’ tab. And Click on the ‘New’ button.
Select 'Daily'
Check "Repeat Task Every" and make it as "1 minutes" and choose for a duration of "Indefnitely"
Check the checkbox ‘Stop the task if it runs longer than’. It is optional. If the script goes in an indefinite loop or a similar situation due to any reason, the task will be terminated automatically after the day/time defined in this option. By default the value is ‘3 days’. Leave the default value.
Click OK
Click on the ‘Actions’ tab and click on the ‘New’ button inside it.
in the Program/Script find the php exe file for eg. C:\wamp\bin\php\php8.2.13\php.exe or C:\wamp64\bin\php\php8.2.13\php.exe
in Add Arguments type C:\wamp\www\vlsm\vendor\bin\crunz schedule:run or C:\wamp64\www\vlsm\vendor\bin\crunz schedule:run
Click on OK
When prompted for password, please enter the Windows user password (might be cphd123, but check with lab first)

4. Setting up Interfacing

Start phpmyadmin by typing http://localhost/phpmyadmin in browser (login id is root and password is mko)(*&^)

Click on SQL menu on top and type the following lines

CREATE DATABASE `interfacing` CHARACTER SET utf8mb4
COLLATE utf8mb4_general_ci;

CREATE USER 'interfaceadmin'@'%' IDENTIFIED
WITH mysql_native_password AS 'interface@12345';

GRANT USAGE ON *.* TO 'interfaceadmin'@'%' REQUIRE NONE
WITH MAX_QUERIES_PER_HOUR 0
MAX_CONNECTIONS_PER_HOUR 0
MAX_UPDATES_PER_HOUR 0 MAX_USER_CONNECTIONS 0;

GRANT ALL PRIVILEGES ON
`interfacing`.* TO 'interfaceadmin'@'%';

This will create a blank interfacing database. Now click on interfacing on left and import the sql file
Download the latest Interfacing executable
Install the executable and login with the credentials admin and admin
On the settings screen, please enter the correct MySQL details and Instrument Interface details
Ensure that the interface shows connected before releasing results from the machine