pynomer

pynomer is a simple python wrapper for nomer. Nomer is a stand-alone java application which maps identifiers and names to taxonomic names and ontological terms.

Installation

Make sure you installed the latest version of nomer, or use the Docker image instead.

$ pip install pynomer

Usage

As a command-line tool

pynomer --help
Usage: pynomer [OPTIONS] COMMAND [ARGS]...

  Options:
    --help  Show this message and exit.

  Commands:
    append              Append term match to row using id and name columns...
    clean               Cleans term matcher cache.
    input-schema        Show input schema in JSON.
    matchers            Lists supported matcher and (optionally) their...
    output-schema       Show output schema.
    properties          Lists configuration properties.
    replace             Replace exact term matches in row.
    validate-term       Validate terms.
    validate-term-link  Validate term links.
    version             Show Version.

As a python module

>>> from pynomer import *
>>> version()
('nomer version', '0.1.21')

With Docker

Build image from source:

git clone https://github.com/nleguillarme/pynomer.git
cd pynomer
docker build -t pynomer:latest .

Run commands in the container:

docker run -v$PWD/.nomer:/.nomer pynomer:latest pynomer append "\tHomo sapiens" -e -o json

|⚠️| When running pynomer append and replace commands in Docker, you have to use the -e option !

As a client-server app

Build server image from source:

docker build -f Dockerfile.server -t pynomer-server:latest https://github.com/nleguillarme/pynomer.git

Run pynomer server:

docker run --rm -v$PWD/nomer:/nomer -p9090:9090 pynomer-server:latest

Create the client:

>>> from pynomer.client import NomerClient
>>> client = NomerClient(base_url="http://localhost:9090/")
>>> client.version()
'0.1.21'

License

License: MIT

Authors

pynomer was written by nleguillarme.