ODAM

Open Data, Access and Mining

ODAM is an Experiment Data Table Management System (EDTMS) that gives you an open access to your data and make them ready to be mined - A data explorer as bonus

For more information, see ODAM: Deployment and User's Guide

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Maintainer: Daniel Jacob - INRAE - UMR 1332 BFP (2017-2021)

Installation

Requirements:

• a recent Linux OS that support Docker (see https://www.docker.com/)

From Github, Clone the repository

    $ git clone https://github.com/inrae/ODAM.git

Then cd to your clone path, and build the docker images (may take a while depending on your network speed and the traffic)

    $ cd ODAM
    $ sh ./odam.sh build

Or you may prefer getting directly the docker images from the official docker repository

    $ cd ODAM
    $ sh ./odam.sh pull

Data Repository

• Create a data repository (i.e. a directory) anywhere your ODAM installation can access it either by a symbolic link or a mount point to a local data directory.

    $ mkdir /opt/DataRepos

• Create / add a dataset into your data repository (see presentation)
• To prepare your own data subsets, see the ODAM: Data collection and preparation

Get the complete FRIM dataset as an example

    $ cd /opt/DataRepos
    $ wget https://data.inrae.fr/api/access/datafile/:persistentId/?persistentId=doi:10.15454/95JUTK/P0ZJMJ -O frim1.zip
    $ unzip frim1.zip
    $ rm -f frim1.zip

Configuration

Edit the ./odam.sh file , change the GETDATA_URL_PROXY, GETDATA_DATAREPOS, GETDATA_PORT and DATAEXPLORER_PORT parameters according to your local configuration

Usage

     Usage: sh ./odam.sh COMMAND

     Commands:
        pull            pull the docker images from the official docker  repository
        build           build the docker images of the web-service 'getdata' and the web application 'dataexplorer'
        start           start the docker containers from their docker image
        stop            stop the docker containers
        ps              view the status of docker containers

Then, start the docker containers

    $ sh ./odam.sh start

Normally if everything is ok, you can access your data via web-services. You can test for example with the command curl (depending on the GETDATA_URL_PROXY and GETDATA_PORT settings in the ./odam.sh file ):

    $ curl "http://myhost.org:8081/query/<your_dataset_name>"

Or test your getData API through the web swagger UI (go to API folder)

In your Web browser, you can launch the Data Explorer connected to your dataset with the URL http://myhost.org:8080/?ds=your_dataset_name (depending on the GETDATA_URL_PROXY and DATAEXPLORER_PORT settings in the ./odam.sh file ).

NGINX configuration (Linux)

For avanced users: In case you would like to use a proxy server, the better is to install and set NGINX, an HTTP and reverse proxy server.

In the /etc/nginx/conf.d/my-site.conf, you should add two 'location' sections as shown below:

server {
    listen 80 default;
    server_name $host;

    ...

   location /getdata/ {
        proxy_set_header Host $host;
        proxy_set_header X-Real-Ip $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_pass http://localhost:8081;
    }

    location /dataexplorer/ {
        proxy_pass http://localhost:8080;
    }

    ...

}

In this way, you can use the URL http://myhost.org/getdata/... for API and the URL http://myhost.org/dataexplorer/... for the data explorer

Future improvements

• A web page allowing users to annotate the attributes with ontologies (based on AgroPortal/BioPortal API)
• Linked Data format / RDF export
• See https://inrae.github.io/ODAM/todo/

Publication:

Daniel Jacob, Romain David, Sophie Aubin, Yves Gibon (2020) Making experimental data tables in the life sciences more FAIR: a pragmatic approach, GigaScience, Volume 9, Issue 12, December 2020, doi:10.1093/gigascience/giaa144

Funded by:

• INRAE UMR 1332 BFP, Bordeaux Metabolomics Facility

License

GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 - See the included LICENSE file.