This repository hosts the code for the blog post: Serve NCBI Taxonomy in AWS, Serverlessly.
It contains two parts. "prepyphy.py" transforms the NCBI taxdmp file into tsv files for import into Aurora. The pyphy-lambda folder contains the Lambda function code for upload into AWS Lambda.
To prepare the tsv files. First download taxdmp from NCBI taxonomy and unpack it. Then run:
python prepyphy.py taxdmp_folder
It will generate two files (tree.tsv and synonym.tsv) in the current folder.
Before you upload the pyphy-lambda, you need to open rds_config.py and fill in the details of your Aurora database.
#config file containing credentials for RDS MySQL instance
endpoint = ""
db_username = ""
db_password = ""
db_name = ""
Once done, zip the files in this folder (please don't zip the folder itself). And the zip file is ready for upload to Lambda.
- Sixing Huang - Concept and Coding