igem-uploads 2.0.0

Helps iGEMers upload their files to the iGEM server.

igem-uploads

Background

Team Wiki has long been a characteristic hallmark of iGEMers. By vividly illustrating and eloquently describing their projects from various angles on accessible websites, all teams can monitor progress and draw inspiration from others. This fosters inter-team collaborations and strengthens connections within the iGEM community. Year after year, Team Wiki has become the most standardized and prevalent portal for teams' projects, delighting people worldwide.

In 2022, iGEM took an innovative step by integrating GitLab, a powerful project management platform. This integration streamlined the project building and release process, but challenges persist in building and maintaining the team wiki.

During the building process, team members frequently commit changes to their IDE (Integrated Development Environment). When these commits impact references to picture resources, team members must also navigate web browsers to add or modify files hosted on uploads.igem.org, in accordance with the policy. This necessitates frequent switching between the browser and their IDE. Moreover, the heavy traffic often strains the network, increasing the risk of the server becoming unreachable.

Description

Our primary aim is to simplify the process for iGEMers when it comes to committing images, reducing the need for constant switching between web browsers and their IDEs. We aspire to provide a more convenient way to access and upload content, allowing wiki builders to focus on creating and designing webpages within their IDE with fewer distractions.

We also aim to enhance the overall user experience with our content hosting site. We will offer a means to access their remote directory without requiring the use of a web browser, thereby reducing the graphical and unrelated content requests and relieving the load on the uploads.igem.org webpage.

In addition, the software must be user-friendly, as we intend to make it easier for all iGEMers to upload their wiki assets, enhance their project illustrations, and better express themselves. It will be designed as cross-platform software, ensuring that wiki builders can deploy it on any operating system, collaborate effectively, and keep their projects on track.

Technical Information

After analyzing the requirements and expectations, we have conceived the idea of developing a console software that is easy to set up and ready to use out-of-the-box. This program will be seamlessly integrated into the console, enabling iGEMers to operate it by simply entering commands within their IDE or system terminal, just a click away.

Python serves as the foundation for our project. Python is a versatile, cross-platform programming language with extensive support libraries and a large, active community base. This choice allows us to quickly prototype and develop our software effectively.

To interact with users, we employ the warnings module to send informative messages to the terminal, and prettytable to format structural data. We import the requests library to send requests and retrieve data from websites, and use etree to parse HTML information. For streamlined file location, we have also incorporated the path module.

Thanks to these powerful Python libraries, we have successfully developed this versatile tool.

Installation

Our software can be easily installed using pypi:

python3 -m pip install igem-uploads

Usage

0. Initial configuration

Log in to igem.org with your username and password registered on the official site.

client = uploads.Session()
client.login('username', 'password')

1. Upload single file to specific directory

You can upload a file in a specified local directory to a remote directory. Files will be uploaded to remote root if you omit the target_directory argument.

client.upload('path/to/file')
client.upload('path/to/file', 'target_directory')

2. Query files/directories in specific directory

To list all files and directories in a directory, simply type the command below. The software will list all items in root directory if directory is omitted.

client.query('')
client.query('directory')

3. Upload directory to specific directory

If you want to upload a directory and its subdirectories to specific directory, you can use upload_dir. All items in the dir you specified will be uploaded to remote root is target_directory is omitted.

client.upload_dir('path/to/directory')
client.upload_dir('path/to/directory', 'target_directory')

4. Delete single file in specific directory

To delete a specific file, call delete with your filename specified.

client.delete('filename', 'file_parent_directory')

5. Truncate directory

To truncate a directory, call truncate and specify it.

client.truncate_dir('target_directory')

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Authors and acknowledgment

• Tianyi LIANG - Building and publishing
• Yi HAN - Testing and documentation

Links

• PyPI
• GitHub
• GitLab