hcrat / cibio-covid

CIBIO Covid Code

CIBIO-COVID

This repo contains the code developed for the intranet system to support the COVID-19 testing operations ad the DMA Lab of the University of Trento. The repo contains two main parts:

• A backend written in Python to allow for the operators to upload analysis files
• A frontend written in PHP/HTML/SQL to organize the data and to provide structured interface to them. This is currently deplyed at http://colab1.cibio.unitn.it:8080/cibio-covid/index.php

Frontend search page: one PCR sample is shown and the PCR curves are shown, together with the COVID-19 test outcome

Requirements

For the frontend (DB sample search):

• PHP 7.2 (frontend)
• MySQL (frontend)

For the backend (data loading):

• Python3
• openpyxl
• mysql-connector-python-rf
• mysql-connector-python

Note: Be sure to uninstall mysql-connector from your python installation (if present) and install mysql-connector-python

Data Visualization

Available within UniTN VPN Here.

It is possible to search:

• By barcode (or comma separated list of barcodes). This also shows the PCR curves for samples processed after May 7th
• By PCR plate (shows the layout of each plate, colored by COVID-Test outcome)
• By PCR date (shows all the PCRs performed on a given date)
• Interative multi-sample search (for barcode-reader equipped PCs in the laboratory area). This also sorts the scanned barcodes into two different lists (positive and negative samples).

Data Upload

Files can be loaded into the Database with an online procedure available from within UniTN VPN available here. Excel templates for data analysis are provided to the data-entry operators by the DMA Staff.

To upload a file, simply load it into the webpage and select the type of template you are loading:

Once the upload is completed you should see a confirmation message like this:

Alternatively, data can be manually loaded with two scripts in Python:

Samples extraction template (extr_estrazioni.py)

extr_estrazioni.py populates the DB with the samples from the "Estrazioni" Excel template. It takes as input a folder with all the Excel files from the estrazioni procedure. The files contain the sample barcode and the date of processing.

usage: extr_estrazioni.py [-h] [--extr_folder EXTR_FOLDER]

optional arguments:
  -h, --help            show this help message and exit
  --extr_folder EXTR_FOLDER
                        path to the "Estrazioni" folder. The folder must
                        contain xlsx or xlsm files from the Estrazioni
                        pipeline. One file for each batch mubst pe provided

Example:

extr_estrazioni.py --extr_folder </path/to/your/extrazioni/folder>/200410/

Will load all the samples stored in 200410

Samples Data Analysis template (extr_data_analysis.py)

extr_data_analysis.py processes Analisi files and populates the DB with the results of each PCR plate on each sample. The files must be in the right format as defined by the template.

usage: extr_data_analysis.py [-h] --data_folder DATA_FOLDER
                             [--platename_from_file]

optional arguments:
  -h, --help            show this help message and exit
  --data_folder DATA_FOLDER
                        his is the folder containing all the Analisi Excell
                        files. One file per plate.

  --platename_from_file
                        allows to take the Plate Name from the filename,
                        instead than from the designated cell in the Excel template

Example:

extr_data_analysis.py --data_folder </path/to/your/analysis/folder>/200410/

Will load all the Analisi files in the folder 200410

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The code and templates in this repository were implemented and designed by Moreno Zolfo, Tarcisio Fedrizzi, Serena Manara and Francesca Demichelis