dspa-database

Code for database upload and database layout.

📦 Current Tables in dynaprotdbv2

mysql> SHOW TABLES;

Table Name
differential_abundance
dynaprot_experiment
dynaprot_experiment_comparison
go_analysis
go_term
organism
organism_proteome
organism_proteome_entries
protein_scores

🚀 Uploading a New Experiment

Use the uploadNewExpweriment/uploadLipExperiment.sh script to upload an experiment folder to the remote VM, run the upload scripts, and clean up afterward.

This script:

1. Copies the experiment folder to the remote VM.

2. Runs the upload scripts metadata.py and proteinScores.py located in the src directory.

3. Ingests files such as:

   • params.yaml

   • qc_plots.pdf

   • differential_abundance_<...>.tsv

   • go_term_<...>.tsv

4. Inserts data into the appropriate MySQL tables.

5. Updates table indexes to ensure good database performance.

6. Cleans up the uploaded folder from the VM after processing.

7. Once complete, the experiment becomes visible at: https://www.dynaprot.org/experiments

🛠 Usage

echo "Usage: ./uploadLipExperiment.sh /path/to/folder vm_username"

./uploadLipExperiment.sh LiP_School9_LiP ekrismer

⚠️ Important

• The MYSQL_PASSWORD is currently set to an empty string in the script for security reasons.

• Do not commit actual passwords or credentials to the repository.

• Instead, export credentials in your shell or use environment files or secrets management tools for production.