The ISA-explorer web application has been developed to provide a visualization of ISATab files and it can be used to host a lightweight ISATab repository. It runs on a Node.js environment and relies on python to load the datasets.
Dependencies
- Node.js 6+
- Python 3.5+
Libraries used:
- FontAwesome 4.3.0
- lunr.js - fast full text search within the browser
- React.js (v0.15)
- Express.js web framework
This code is made available with BSD 3-Clause License.
Simply clone the repository, or download it as a zip file.
We recommend running the python scripts using a virtual environment.
-
If not already installed in your system, first install the virtual environment via
pip:pip install virtualenv -
Create a virtual environament:
virtualenv venv -
Then, activate the virtual environment:
source venv/bin/activateif you are using the bash shell or . venv/bin/activate if you are using /bin/sh
- Install the requirements:
pip install -r requirements.txt
or
pip install --upgrade -r requirements.txt
if you want to upgrade the requirements already installed.
To download Springer Nature Scientific Data files, run the sdata_crossref_download.py script:
python scripts/sdata_crossref_download.py
Or to use your own data, place your ISA-Tab files in the Data directory (can also be symlinks).
To build a new index over the files, run the build_index.py script, which will build an initial metadata repository JSON file that is used by lunr.js to search, and by the web application to present the initial file list.:
python scripts/build_index.py data
This will create a file called isatab-index.json which will be read by the application to generate the search interface.
To generate the json-ld with schema.org representation, use:
python scripts/schemaorg_conversion.py
To install dependencies:
npm install
To build the assets locally:
npm run build:local
(check other builds in package.json)
To run the web server:
node server.js
- Gonzalez-Beltran, Alejandra's post in Scientific Data blog
- Gonzalez-Beltran, Alejandra's slides Data Publication: Discover, Explore, Visualise presented at the Data Visualisation and the Future of Academic Publishing meeting organised by the University of Oxford and Oxford University Press on June 10th 2016.
- Gonzalez-Beltran, Alejandra; Maguire, Eamonn; Khodiyar, Varsha; Rocca-Serra, Philippe; Johnson, David; Izzo, Massimiliano; et al. Find me the data - Discover and explore Springer Nature’s Scientific Data datasets with the ISA-explorer tool presented at Force2016