Add Script For Rendering The Results Locally

Introduction

In the world of bioinformatics and data analysis, having a seamless way to preview results is crucial for efficient workflow management. Currently, the process of previewing results for the task_cyto_batch_integration task involves a series of manual steps, including cloning repositories, editing scripts, and committing changes. In this article, we will explore the creation of a simple script that can be run to get a local preview of the results, making it easier for anyone to access and visualize the data.

Understanding the Current Workflow

Before we dive into creating the script, let's take a closer look at the current workflow. After running the scripts/run_benchmark/run_full_seqeracloud.sh script and generating new results (e.g., s3://openproblems-data/resources/task_cyto_batch_integration/results/run_2025-03-12_11-23-51), the following steps are taken to preview the results:

• Clone the repositories: git clone openproblems-bio/openproblems and git clone openproblems-bio/website
• Switch to the add-cyto-batch branch: In the website repository, switch to the add-cyto-batch branch
• Edit the run_test.sh script: In the openproblems repository, edit the src/reporting/process_task_results/run_test.sh script to set the for loop to for TASK in "task_cyto_batch_integration"; do
• Run the run_test.sh script: Run the src/reporting/process_task_results/run_test.sh script
• Commit the changes: Commit the changes to the website to get it to preview the results

Creating a Simple Script for Local Preview

To simplify the process of previewing results, we can create a script that automates the above steps. This script will be called local_preview.sh and will be placed in the scripts directory of the openproblems repository.

Step 1: Create the local_preview.sh Script

Create a new file called local_preview.sh in the scripts directory of the openproblems repository. Add the following code to the file:

#!/bin/bash

# Clone the repositories
git clone openproblems-bio/openproblems
git clone openproblems-bio/website

# Switch to the `add-cyto-batch` branch
cd website
git checkout add-cyto-batch

# Edit the `run_test.sh` script
cd ../openproblems
sed -i 's/for TASK in ".*"; do/for TASK in "task_cyto_batch_integration"; do/' src/reporting/process_task_results/run_test.sh

# Run the `run_test.sh` script
cd src/reporting/process_task_results
./run_test.sh

# Commit the changes
cd ../website
git add .
git commit -m "Preview results for task_cyto_batch_integration"

Step 2: Make the Script Executable

Make the local_preview.sh script executable by running the following command:

chmod +x scripts/local_preview.sh

Step 3: Run the Script

To run the script, navigate to the scripts directory and execute the following command:

./local_preview.sh

This will automate the process of previewing results for the task_cyto_batch_integration task.

Benefits of the Script

The local_preview.sh script offers several benefits, including:

• Simplified workflow: The script automates the process of previewing results, making it easier for anyone to access and visualize the data.
• Reduced manual effort: The script eliminates the need for manual steps, such as cloning repositories, editing scripts, and committing changes.
• Improved efficiency: The script saves time and effort, allowing users to focus on analyzing the data rather than managing the workflow.

Conclusion

Q: What is the purpose of the local preview script?

A: The local preview script, local_preview.sh, is designed to automate the process of previewing results for the task_cyto_batch_integration task. It simplifies the workflow by eliminating the need for manual steps, such as cloning repositories, editing scripts, and committing changes.

Q: How do I run the local preview script?

A: To run the script, navigate to the scripts directory and execute the following command:

./local_preview.sh

Q: What are the system requirements for running the local preview script?

A: The script requires a Unix-like operating system, such as Linux or macOS, and a Git repository manager. It also requires the sed and git commands to be installed and available on the system.

Q: Can I modify the script to preview results for other tasks?

A: Yes, you can modify the script to preview results for other tasks by editing the TASK variable in the script. For example, to preview results for the task_cyto_batch_integration task, you would set the TASK variable to "task_cyto_batch_integration".

Q: How do I troubleshoot issues with the local preview script?

A: If you encounter issues with the script, you can try the following troubleshooting steps:

• Check the script's output for any error messages.
• Verify that the script has the necessary permissions to run.
• Ensure that the script is running in the correct directory.
• Check the Git repository for any conflicts or issues.

Q: Can I use the local preview script with other Git repository managers?

A: The script is designed to work with Git repository managers, but it may require modifications to work with other repository managers. You can try modifying the script to work with your repository manager, but it may require additional configuration and testing.

Q: Is the local preview script secure?

A: The script is designed to be secure, but as with any script, there is a risk of security vulnerabilities. You should review the script's code and ensure that it is up-to-date and secure before running it.

Q: Can I contribute to the development of the local preview script?

A: Yes, you can contribute to the development of the script by submitting bug reports, suggesting improvements, or contributing code changes. You can contact the script's maintainers or submit a pull request to the script's repository.

Q: Where can I find more information about the local preview script?

A: You can find more information about the script on the script's repository page or by contacting the script's maintainers. You can also search for online resources and tutorials that provide more information about the script and its usage.