ELAB LOADER Beta V 1.6.0

• ELAB LOADER Alpha V0.5.8
  • Introduction
  • Installation
  • Getting started
  • Data preparation
  • Modes
  • Mode seqp
  • Mode qpcr
  • Mode rest
  • Mode plas
  • Mode cons
  • Running
  • Arguments and Flags
  • Command examples
  • Legal and Credits <!-- TOC -->

Introduction

This is ELABLOADER, a simple-to-use, no-bullshit, non bloating, console based solution to transfer data between the API provided by elabFTW and tables provided by the physical lab.  It is utilized mainly by reading prepared XLSX, CSV, or TXT files.  The current version is under development. Please report any bugs! Thanks!

Only works with elabFTW installed A demo version of elabFTW is available at https://demo.elabftw.net/

Installation

You must have Python 3.9 with the following libraries installed

• elabapi_python
• pandas
• numpy
• progress
• validators

Github is the official download source, the place to praise, and the place to complain: Simply clone the project, and you should be good to go. 

git clone https://github.com/KJPMolgenLab/ELAB_LOADER.git

Install the required packages vie pip

pip install -r requirements.txt

Getting started

What do I need? - The elabFTW URL to the API - e.g. https://demo.elabftw.net/api/v2 - Also, kindly ask your administrator if unsure

- an API Key - can be generated in the user panel - needs to have write permission - Online information see Info - Kindly ask your administrator if unsure

• The Category ID of the type of item you want to update in Elab:
  • The type of item has to be predefined in the labbook
  • If you select the type of item in your database view you can get the id from the url
  • e.g. https://demo.elabftw.net/database.php?q=&cat=7&mode=show&limit=15 gives category 7
  • And you guessed it ask your Admin if unsure

Data preparation

First, carefully prepare a list of the items to be added in XLSX format (Excel sheet). We strongly suggest using XLSX for comforts sake. Make sure the mandatory columns and header names are present in the file. These vary between the different types of data you can upload. For the different modes we provided templates in the Example folders

Everything marked red in the ./Examples Excel files is a mandatory entry and is case SENSITIVE!

You can add as many columns as you wish, they will be added to the items in tabular format

Fill out the mandatory columns. It is recommended to also fill out the existing ones, or remove them if not needed. Any additional columns will be added into the Elab table. Results can vary due to Elab's CSS.

Modes

Mode seqp

This mode will upload sequencing primers onto Elab. The algorithm will check if the primer sequence already exists in the database, if yes the program does not upload or change the primer again and give you feedback about it If the Primer sequence cannot be identified a new entry is generated

Mode qpcr

This mode will upload qpcr primers onto Elab. The template here assumes a primer pair and a Probe If you do not have a Probe in your qPCR designs just leave the column empty

Similarity check will be done on the sequences of the primers and the probe Identical items will be patched, i.e. replaced by the information in the table If no item can be identified to be similar a new entry is generated

Mode rest

This mode will upload restriction enzymes onto Elab. Similarity check will be done based on the Supplier and the Ordernumber If the Restriction enzyme cannot be identified a new entry is generated, otherwise the item is skipped with a feedback

Mode plas

This mode will upload plasmids onto Elab. Similarity check will be done based on the Name/title of the entry If the Plasmid cannot be identified a new entry is generated, otherwise the item is skipped with a feedback

Mode cons

This mode will upload consumables (e.g. Chemicals, Tools, etc.) onto Elab. Similarity check will be done based on the Supplier and the Ordernumber. If the Restriction enzyme cannot be identified a new entry is generated, otherwise the item is skipped with a feedback

Running the algorithm

to test if your program runs go to a command line terminal move to the folder of the Elabloader and check is the elabloader.py file is executable

commandline cd <PathtoElabloader> ./elabloader.py if all libraries are installed successfully the following message should appear

```commandline All libraries loaded and ready

         ______ _               ____  _      ____          _____  ______ _____  
        |  ____| |        /\   |  _ \| |    / __ \   /\   |  __ \|  ____|  __ \ 
        | |__  | |       /  \  | |_) | |   | |  | | /  \  | |  | | |__  | |__) |
        |  __| | |      / /\ \ |  _ <| |   | |  | |/ /\ \ | |  | |  __| |  _  / 
        | |____| |____ / ____ \| |_) | |___| |__| / ____ \| |__| | |____| | \ \ 
        |______|______/_/    \_\____/|______\____/_/    \_\_____/|______|_|  \_\

no arguments provided type --help for more information

```

Arguments and Flags

The program needs arguments to work; so-called "Flags". These are instructions you give via a dash. The following instructions are available and mandatory.

Please make sure you do not miss any, or the program will report back an error:

``` -k, --apikey API key as generated on the ElabFTW user panel needs to have write and read access

-u, --url to parse the url of the elab page.

-f, --file , File ending accepted is .XLSX

-c, --cat_id to parse the numeric(int) category ID of the DB type you wish to upload. This can be found out on ELAB. In case of questions ask your administrator.

-m, --mode to select between type of import.

                Modes available:

                olig    uploads Oligos for sgRNA generation
                plas    uploads Plasmid information 
                rest    uploads restriction enzyme information 
                seqp    uploads Sequencing primer information
                qpcr    uploads qpcr primer information
                cons    uploads consumable information 

                Each mode needs to be provided with a table one at a time. 
                The table needs to fulfill all the requirements found
                in the readme.md and the ./Example folder to work properly.

```

Command examples

Now that you have learned about the flags, it's time to finally send the command. In the "Terminal", enter the following:

shell ./elabloader.py [Flags]

Before you ask, here is a pre-fabbed command:

shell ./elabloader.py --apikey <enteryourkey> \ --url <https://yourelab.yourelabsending.lab/api/v2/> \ --file <./Example/Example_cons.xlsx> \ --cat_id <numberofyourcatid>

For logging, you can dump the output to a file. shell ./elabloader.py --apikey <enteryourkey> \ --url <https://yourelab.yourelabsending/api/v2/> \ --file </files/ForEndusers/ElabLoader/Input/example.xlsx> \ --cat_id <numberofyourcatid> > Debug/output.log

Legal and Credits

This Script is published under BSD-3-Clause Year 2024 Copyright Holder A. Chiocchetti

ELABLOADER was created by:

• achiocch
• LF-KGU