Docker Compose file to manage the build and deployment of MTW-MeSH, an app developed for the National Medical Library (NML, Prague, Czech Republic) for the translation of MeSH vocabulary (Medical Subject Headings).
This Compose file make uses of this Jena Fuseki docker image.
This repository has three branches :
Contents
Install Docker Desktop for Windows and macOS.
Clone the repository:
git clone https://github.com/Inserm-IST/MTW-MeSH-Docker.git
Move into the new directory :
cd MTW-MeSH-Docker/
These operations are only necessary before the first launch.
All modified files are saved to volumes, so as long as the volumes are persisted (including moving to a new release, removing the containers etc.) it's not necessary to re-run these operations.
Important values are marked with !
Modify the values for your personal configuration, including TARGET_YEAR
, TARGET_LANG
, TARGET_NS
etc.
Make sure this line is uncommented :
SPARQL_HOST = http://jena_fuseki:3030/
For more details, refer to MTW-MeSH Wiki
A default value is provided for the admin pass for both MTW and Jena Fuseki as a secret in the admin_settings.txt
file.
:warning: Warning: Make sure to change this value and not to reveal then content of this file (via git for example).
docker compose build
For more details see: Loading MeSH datasets
Copy the official annual RDF dataset and your RDF translation dataset to the ./mesh-data/
directory.
Make sure to validate your mesh.nt.gz
and mesh-trx_YYYY-MM-DD.nt.gz
file with riot
.
You can for example use the Jena Docker image :
docker run --rm \
--volume /$(pwd)/mesh-data/:/rdf \
stain/jena riot --validate mesh.nt.gz mesh-trx_YYYY-MM-DD.nt.gz
A special service called staging
is part of the Compose file to load the MeSH data into the triple store.
:warning: Warning: All the data already present in the Mesh dataset in Jena Fuseki will be lost.
Type the following command:
docker compose run --rm staging
docker compose up -d
Using Traefik/Caddy as reverse proxy:
Without reverse proxy:
For more details see: MeSH Annual Updates
In the fuseki interface, in the Manage
tab, click on the backup
button for the mesh dataset.
You should now have a backup file mesh_YYYY-MM-DD_....nt.gz
in the backups
folder of the mtw_fuseki-data
volume.
If we want to save this mesh_YYYY-MM-DD_....nt.gz
file from the Docker volume to our local mesh-data
folder, we can use the following command:
docker cp mtw-jena_fuseki-1:/fuseki/backups/mesh_YYYY-MM-DD_....nt.gz ./mesh-data/
curl https://nlmpubs.nlm.nih.gov/projects/mesh/rdf/mesh.nt.gz --ssl-no-revoke -O
Validate the backup mesh_YYYY-MM-DD_....nt.gz
and the official MeSH RDF dataset mesh.nt.gz
with riot
.
If the mesh_YYYY-MM-DD_....nt.gz
and mesh.nt.gz
files are stored in our local mesh-data
folder, we can use the Jena Docker image :
docker run --rm \
--volume /$(pwd)/mesh-data/:/rdf stain/jena \
riot --validate mesh.nt.gz mesh_YYYY-MM-DD_....nt.gz
docker run -it --rm \
--volume /$(pwd)/mesh-data/:/rdf \
--workdir //rdf mtw-server \
python3 //app/tools/mesh-nt2trx.py mesh_YYYY-MM-DD_....nt.gz
You should now have a translation file mtw-trx_YYYY-MM-DD.nt.gz
in your local mesh-data
folder.
In the fuseki interface, in the Manage
tab, click on the remove
button for the mesh dataset.
docker compose down
Follow the steps in Loading the MeSH datasets
docker run -it --rm \
--volume mtw_mtw-data:/app/instance/ \
--workdir //app/instance/ \
mtw-server bash
apt-get update && apt-get install nano
nano conf/mtw-dist.ini
Update the values TARGET_YEAR
, PREV_YEAR_DEF
, PREV_YEARS
according ro your configuration.
Save and exit: CTRL+S
, CTRL+X
rm cache/*
exit
docker compose up -d