Pre-requisites
1. Start the database server
Before you start exploring and querying the database, you must start the
database server (if it isn't running yet). For that, use the following
parsomics-cli command:
parsomics database start
If in doubt, append --help to the command:
parsomics database start --help
You can read more about the database start command and its options in the
Managing the database section of the
Usage documentation.
2. Populate the database
To populate the database with your data, write your parsomics configuration
file run the following parsomics-cli command:
parsomics analysis run
If in doubt, append --help to the command:
parsomics analysis run --help
Again, you can read more about the analysis run command and its options in
the Running the analysis section of
the Usage documentation.
3. Start the REST API server
If you wish to use the REST API, you must also start the REST API server. To do
that, first make sure the parsomics-api-server package is installed. This
package is bundled in the parsomics metapackage, so you already have it
if you followed the installation guide.
Start the database server with the following command:
fastapi run <path-to-parsomics-api-server-installation>
For example, if you are using venv:
fastapi run .venv/lib/python3.12/site-packages/parsomics_api_server
If in doubt, append --help to the command:
fastapi run --help
You can read more about the fastapi command at the FastAPI
CLI section of the
FastAPI documentation.
FastAPI is the main Python library that was used in the making of
parsomics-api-server.