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Deploy Morph-xR2RML with Docker

You can deploy Morph-xR2RML along with a MongoDB database using Docker.

First make sure your have docker-compose or install it.

If you have cloned this repository, just skip the next step. Otherwise, download file xr2rml_docker.zip, and unzip it to the directory from where you will run docker-compose. From a Linux terminal that would be:

wget https://github.com/frmichel/morph-xr2rml/raw/master/docker/xr2rml_docker.zip
unzip xr2rml_docker.zip

Set file access rights as shown below:

chmod -R 755 mongo_import
chmod -R 755 xr2rml_config
chmod -R 777 log
chmod -R 777 mongo_db
chmod -R 777 xr2rml_output
chmod 777 run.sh

Then run:

docker-compose up -d

Now, both containers are started and ready to process data.

Script run.sh provides an example of how to run the different steps manually: (1) import data located in mongo_import into MongoDB, and (2) run Morph-xR2RML to translate the data to RDF and store the result in xr2rml_output.

Description of each folder

  • mongo_db: will contain the actual Mongo database, so that you don't need to re-import files everytime you rerun Morph-xR2RML.
  • mongo_tools: set of handy bash scripts to import json/csv/tsv data into MongoDB.
  • mongo_import: copy your files to import in this folder, it is moutned in the MongoDB container.
  • xr2rml_config: mapping files (morph.properties, log configuration file) and bash scripts to run Morph-xR2RML. This folder is mounted in the Morph-xR2RML container.
  • xr2rml_config: where the RDF files will be written.
  • run.sh: example script showing how to use evrything from your machine, i.e. to import data into MongoDB and run Morph-xR2RML to translate the data to RDF.

Accessing Logs

The docker-compose.yml mounts the Morph-xR2RML log directory to the Docker host in directory log. Check it if an error occurs or if your mapping does not generate the expected triples.

Changing Morph-xR2RML configuration and mappings

Put your mapping files in folder xr2rml_config. Script xr2rml_config/run_xr2rml.sh will be used to run the transltation from within the container.

Mapping files can also be templates, with 2 predefined placeholders: {{collection}} and {{dataset}}. Script xr2rml_config/run_xr2rml_template.sh will replace them before running the translation. Check the example mapping xr2rml_config/mapping_movies.ttl and how it is used by script run.sh.

The main Morph-xR2RML configuration file is editable at xr2rml_config/morph.properties. In particular that's where you would change the name of the MongoDB database.

Importing data into MongoDB

Script mongo_tools/import_tools.sh provides various handy function to import json/csv/tsv data into MongoDB. The data can be imported all at once, file by file, or grouping files to comply with the maximum import size of MongoDB.

Scripts mongo_tools/import-file.sh and mongo_tools/import-json-files.sh provide examples of how to use those functions. They can be used as is, as shown in script run.sh.

Common issues

log or mongo_db directory not writable

The containers need to write in directories log and mongo_db. They will fail if you do not set rights 777 (chmod 777 <dir name>).

SLF4J messages at Morph-xR2RML startup

When it starts up, Morph-xR2RML shows the messages below. They are just warning, you can safely ignore them.

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.