visualization for nanomine project
Note: if installing on a virtual machine, be sure to allocate at least 8G Memory, 2 CPUs and 50G Disk
bash < <(curl -skL https://raw.githubusercontent.com/tetherless-world/whyis/master/install.sh)
- whyis will be installed in /apps/whyis
- install NanomineViz app following:
cd /apps sudo git clone https://github.com/Duke-MatSci/NanomineViz.git cd /apps/NanomineViz/data sudo wget https://raw.githubusercontent.com/Duke-MatSci/nanomine-ontology/master/xml_ingest.setl.ttl sudo wget https://raw.githubusercontent.com/Duke-MatSci/nanomine-ontology/master/ontology.setl.ttl sudo chown -R whyis:whyis /apps/NanomineViz sudo su - whyis cd /apps/NanomineViz pip install -e . exit sudo service apache2 restart sudo service celeryd restart sudo su - whyis cd /apps/whyis python manage.py createuser -e (email) -p (password) -f (frstname) -l (lastname) -u (username) --roles=admin python manage.py load -i /apps/NanomineViz/data/viz.ttl -f turtle cd /apps touch .netrc - after you create the .netrc file under /apps, you need to edit this file.
machine some_url (like 000.000.000.000 or nanomine.oit.duke.edu) -- this is the address of the nanomine server login some_username (like testuser1) password some_password (like testpwd1) - after you edit the .netrc file, in your terminal type:
- the xml_ingest.setl.ttl file references the nanomine server protocol, address and port and may need to be edited
cd /apps/whyis python manage.py load -i /apps/NanomineViz/data/ontology.setl.ttl -f turtle python manage.py load -i /apps/NanomineViz/data/xml_ingest.setl.ttl -f turtle- The load process can be monitored with 'sudo tail -f /var/log/celery/w1.log'
- go to http://localhost/ to login with your credentials during "createuser" command
- go to http://localhost/viz to access the visualization
Each time a change is made on the visualization, apache2 and celeryd service have to be restarted manually. This is very troublesome. whyis has a developing mode that help you allevate this pain.
sudo su - whyis
cd /app/whyis
python manage.py runserver -h 0.0.0.0
The visualization then will be accessed on "http://localhost:5000/viz". Then, you only need to refresh your webpage to see your changes immediately after you make changes to the visualization. After you finished the visualization changes, you can shutdown the developing mode with CTRL+c. Then you have to restart apache2 and celeryd service by
sudo service apache2 restart
sudo service celeryd restart
After this, the updated visualization app will show up at "http://localhost/viz".