Virtual Interface for Production & Experimental Research

Easy | Modular | Lightweight

A simple, highly scalable & adaptable LIMS system for rapidly evolving laboratory teams.

Features

• Customisable clientside: Build your own VIPER modules in Python and help from Boa Constructor
• Boa Constructor: Make new HTML-Javascript-Python front-end modules with simple drag and drop
• Client Scripting: Beginner friendly code with complete control for advanced programmers
• Client Commands: Scriptable client to server requests passed through Server Methods
• Server Methods: Programmable permission authenticated serverside functions
• Security: OAuth2 user verification and encrypted HTTP requests
• SQL: Intrinsic support for MySQL, PostgreSQL and SQLite
• OAuth2: Intrinsic support for Github and LinkedIn OAuth2 Apps

The Vision

• Lightweight plug-and-play framework
• Power for beginner programmers
• Freedom for advanced programmers
• Competency based permissions

Installation

Desktop Installation

Requires Python (>=3.7)

Operating System terminal:

pip install VIPER_LIMS

Python terminal or script:

import VIPER_LIMS
VIPER_LIMS.Install()

Please see the Server Installation Guide or Client Installation Guide below.

Alternatively: download this repository and run VIPER_Installer/VIPER_LIMS/VIPER_Installer.py

Android Installation

Only the VIPER_Client is available for Android; it is not advised to run a VIPER_Server from Android devices.

1. Install Termux from Github or FDroid
2. In the Termux app run the following commands in order, whilst reading and accepting appropriate requests:
   pkg install python
apt update
apt upgrade
pkg install python-cryptography
pip install VIPER_LIMS
python3
import VIPER_LIMS
VIPER_LIMS.Install()
   Please see the Client Installation Guide below and type exit() when you are finished.

Once the installation is complete you can run the VIPER_Client through Termux with the command:
python3 VIPER_Client/VIPER_Client.py

Optional
Set up a custom command so VIPER is easier to launch:
nano .bash_profile
alias viper='python3 VIPER_Client/VIPER_Client.py'
(now press ctrl + x to exit and approve the changes, then restart Termux)

With your custom bash script you can launch the VIPER_Client by running: viper

Updating on Android

To update VIPER_Client from Android you should run -rm rf VIPER_Client
Then to reinstall run the Android Installation commands above from python3 onwards, selecting "no" when prompted to use local source.

Server Installation Guide

Server Install Tutorial

Store the VIPER_Server will need: information from the SQL Database and OAuth 2.0 Service sections below
Run the following command and provide the requested information: VIPER_LIMS.Install("Server")

Server IP Address:

Before you start you should know the local IP of your VIPER_Server.
Use ipconfig on Windows or ifconfig on Unix based systems and get your IPV4 local IP address (usually 192.168.X.X)
If you do not intend to host your VIPER_Server online then your VIPER_Server IP Address will be this local IP

If you want your VIPER_Server to be accessible through the internet you need to Port Forward TCP 8000 on your router to the local IP of your VIPER_Server
Afterwards use your public IP Address

You will use this IP address for the OAuth2 service callback URL. If your IP Address changes you must update the callback URL.

SQL Database

The database which your LIMS requests will access.
MySQL is recommended but PostgreSQL or SQLite should be compatible

The VIPER_Server will need:

• Username
• Password
• IP Address of SQL Server
• Port of SQL Server (default is 3306 for MySQL)

OAuth 2.0 Service

The service which hosts your users accounts, pick ONE:

• LinkedIn OAuth2
• Github OAuth2
• Other available services which require manual configuration
• Further reading if you want to set up your own

The VIPER_Server will need:

• Client ID
• Client Secret
• Callback URL

Client Installation Guide

Client Install Tutorial

1. VIPER_LIMS.Install("Client")
2. Paste the desired deployment folder directory
3. Paste the VIPER_Server SDump (or "none" if you do not have one yet)
4. To connect to a new Server go to Settings_Panel -> Local_Settings, then Paste an SDump -> Click Autosetup SDump
5. Type off or on and click Set ServerURL to disable or enable online mode
   To Logout go to Settings_Panel/Logout AND Logout of your OAuth2 Service Client Tour Tutorial

Applications

Boa Constructor

Build your own modules: Boa Constructor Tutorial

Highly modular, simple, completely customisable scripts for rapidly evolving teams

1. Launch the Client
2. Assemble an HTML page using Boa Constructor
3. See Coding a Module_Script.py
4. Activate your module in Settings_Panel/Module_Toggler
5. Restart VIPER_Client

Coding a Module_Script.py:

Expired_Ethanol_List = LIMSQuery(False, "Reagents", ["Ethanol","Expired"], "fetchall_criteria")) #Access the LIMS SQL Database

Which could execute the following on the server through a fetchall_criteria Method:

SELECT * FROM Ethanol WHERE Expired = True

In this example we are fetching all Expired Reagents:
LIMSQuery(
False: Initiates LIMSQuery's Third Party App support,
Database: The database within which to execute the SQL process,
Command: The data necessary to perform the request,
Method: The VIPER_Server method through which the Command will be processed,
)

#Example Boa Constructed module script:
def Process_User_Request(request):  #Runs when the user clicks a button on your Boa Constructed VIPER Module
    try:
        ButtonPressed = request.form['SubmitButtonPressed']  #Which action button has the user pressed?
        if ButtonPressed == "Button 0":                      #If the user pressed Action button 0 run the following
##YOUR CODE: ##
            Textbox_2 = request.form.get("Textbox 2")             #Input: The user's Textbox 2 input (e.g "Ethanol")
            Textbox_3 = request.form.get("Textbox 3")             #Input: The user's Textbox 3 input (e.g "Expired")

            ##Process the input however you want!##
            Expired_Ethanol_List = LIMSQuery(request,"Reagents", [Textbox_2,Textbox_3], "fetchall_expired") 
            SubmissionResponse = {"Label 4":Expired_Ethanol_List} #Output: Change the text in Label 4

        elif ButtonPressed == "Button 1":                 #if the user pressed a different button...
            #etc
##END OF YOUR CODE##
    except:
        return 'An error has occured.', 400 #If nothing happens, return nothing
    finally:        
        return jsonify(Info=SubmissionResponse) 

Jupyter Notebook integration:

Enable Third Party App Integration in Settings_Panel/Local_Settings

import sys, requests #required imports
VIPERFolder = requests.post("http://127.0.0.1:7800/RefreshLogin", data="locate") #get VIPER_Utility folder
print(f"VIPER Folder: {VIPERFolder.text}")
sys.path.insert(0, VIPERFolder.text) #Prepare VIPER folder for importation
from VIPER_Utility import LIMSQuery #Import VIPER_Utility from VIPER_Client

print( LIMSQuery(request,"Reagents", [Textbox_2,Textbox_3], "fetchall_expired") )