TOXsIgN

Status

In development

Installation

Download the code, then

python setup.py develop

Configuration

Copy development.ini.template to development.ini then fill app:main section parameters

admin contains the list of site administrators (emails, comma separated)

Run

Development

pserve development.ini

Production

pserve production.ini

Create a user

It is possible to create a user via command line to avoid email validation

python create_user.py --config development.ini --email test@test1 --pwd test

Docker

Start mongodb, then the toxsign container. In development.ini, set mongodb hostname to corresponding mongo container name (here toxsign-mongo)

docker run --name toxsign-mongo -d mongo
docker run --name toxsign-elasticsearch -d elasticsearch
docker run --name toxsign-web --link toxsign-elasticsearch:toxsign-elasticsearch  --link toxsign-mongo:toxsign-mongo -v path_to/development.ini:/opt/toxsign/development.ini -p 6543:6543 osallou/toxisgn:dev

For data persistency, you should mount a volume to :

/opt/toxsign/var/upload ( -v path_to_storage:/opt/toxsign/var/upload )

To create a user:

docker exec toxsign-web python create_user.py --config development.ini --email test@test --pwd test

Manual:

docker run --link toxsign-mongo:mongo -v path_to/development.ini:/opt/toxsign/development.inii -it -p 6543:6543 --entrypoint /bin/bash osallou/toxisgn:dev
#>pserve development.ini

Commands

##Database gestion

To reset database :

mongo chemsign2 --eval "db.signature.drop()"

To reset ElasticSearch indexes:

curl -XDELETE localhost:9200/toxsign

##Upload website Docker run :

docker -H 127.0.0.1:2375 run -d -p 6543:6543 -v /home/genouest/bioinfo/irset/toxsign:/opt/toxsign  --link toxsign-elasticsearch:toxsign-elasticsearch --link toxsign-mongo:toxsign-mongo --name toxsign-webapp toxsign-web gunicorn  -p toxsign.pid --log-config=/opt/toxsign/production.ini --paste /opt/toxsign/production.ini

Execute commands in container:

docker -H 127.0.0.1:2375 exec -it 6ac4fbd53605 /bin/bash

##Local access

192.168.1.218

Prepare Ontologies

Use .obo files and run :

wish8.6 convert_OBO.tcl fileIN FileOut

Special process for ChEBI (download chebi_core.obo): next run

python formatChebi.py

For other files :

python prepOnto.py