Introduction
This document provides instructions for using two Python scripts that interact with the OpenSpecimen API to reserve and unreserve specimens. These scripts accept a CSV input file and perform the necessary actions using OpenSpecimen’s API endpoints.
The two scripts included are:
reserveSpecimens.py: Reserves the specimens based on the information in the CSV file.
unreserveSpecimens.py: Unreserves the specimens based on the information in the CSV file.
Prerequisites
Before running the scripts, ensure that you have the following:
Python 3.x installed on your system.
The required Python libraries (e.g.,
requests) installed.Access to the OpenSpecimen API with admin credentials.
A valid CSV input file with the distribution protocol and specimen ID to be reserved or unreserved.
Parameters
The scripts accept four parameters:
OpenSpecimen API URL: The URL where your OpenSpecimen instance is hosted.
Username: The username for logging into OpenSpecimen.
Password: The password for logging into OpenSpecimen.
CSV File: The CSV file containing the distribution protocol and specimen ID information.
Example CSV Format:"Distribution Protocol","Specimen Identifier" "DP1",13627 "DP1",5273 "DP2",738 "DP2",17283
Reserve Specimens Script
This script reserves specimens based on the distribution protocol and specimen ID provided in the CSV input file.
Script | |
How to run? | python3 reserveSpecimens.py ‘<SERVER_URL>' '<USER_NAME>' '<PASSWORD>' '<CSV_FILE>' |
Unreserve Specimens Script
Script |
|
How to run? | python3 unreserveSpecimens.py ‘<SERVER_URL>' '<USER_NAME>' '<PASSWORD>' '<CSV_FILE>' |
To generate the CSV file you can create a OpenSpecimen Query module.
Steps to create a parametrized query to get distribution protocol short title and specimen identifier are:
A. Login to OpenSpeicmen → Navigate To → Query → Create
B. Select Specimen → Label → ALL as shown in the below image.
C. Click on View Records → Actions → Columns → Select Only Needed Columns → Done
Output:
