A python wrapper for nomer
Project description
pynomer
.. image:: https://img.shields.io/pypi/v/pynomer.svg :target: https://pypi.python.org/pypi/pynomer :alt: Latest PyPI version
pynomer <https://github.com/nleguillarme/pynomer>
_ is a simple python wrapper for nomer <https://github.com/globalbioticinteractions/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$PWD/.nomer:/.nomer pynomer:latest pynomer append "\tHomo sapiens" -e -o json
|:warning:| When running pynomer append and replace commands in Docker, you have to use the -e option !
As a client-server app
Build server image from source: ::
docker build -f Dockerfile.server -t pynomer-server:latest https://github.com/nleguillarme/pynomer.git
Run pynomer server: ::
docker run --rm -v$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 <nicolas.leguillarme@univ-grenoble-alpes.fr>
_.
Project details
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