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
Libraries used:
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/activate
if 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