| Name | Query form VPN IP | Endpoint (http API) VPN IP | Query form public IP | Endpoint (http API) public IP | Comments |
|---|---|---|---|---|---|
| Ontop | http://10.14.28.137:8080 | http://10.14.28.137:8080/sparql | http://128.176.233.7:8080 | http://128.176.233.7:8080/sparql | |
| Fuseki | http://10.14.28.137:3030/#/dataset/OME/query | http://10.14.28.137:3030/OME/sparql | http://128.176.233.7:3030/#/dataset/OME/query | http://128.176.233.7:3030/OME/sparql | |
| Virtuoso | http://10.14.28.137:8890/sparql | http://10.14.28.137:8890/sparql | http://128.176.233.7:8890/sparql | http://128.176.233.7:8890/sparql |
- Download: https://dlcdn.apache.org/jena/binaries/apache-jena-5.2.0.tar.gz
- Unpack into a directory and append //dir/to/apache-jena-5.2.0/bin// to $PATH (on *N*X.)
rsparql --service http://128.176.233.7:8080/sparql --query 01-list_of_attributes.rqThe script queries/timer.sh runs a given query N times, measure wall clock, user, and system time and report the resulting statistics. Timings will be saved to disk. Usage (must be in the queries/ directory):
./timer.sh QUERY ENDPOINTURL ENDPOINTNAME NQUERIES
cd queries ./timer.sh 01-list_of_attributes.rq http://128.176.233.7:8080/sparql ontop 100
This would run the query 01-list_of_attributes.rq on the ontop endpoint and write results to 01-list_of_attributes.ontop.timings.csv.
The notebook queries/analyze_timings.ipynb loads all timing csv data, performs some descriptive statistics and renders a number of plots. Adjust to your liking. Required python packages:pandas, seaborn, matplotlib.
Mappings are defined in the
omero-ontop-mappings
repo. The repo is cloned on the Münster server. Ontop runs inside a
screen session and normally restarts after a change to the mappings,
ontology, or config. It may become neccessary to restart ontop in case
of syntactical errors in any of these files. To (re-)launch the ontop
server:
screen -dr ontop cd /home/ubuntu/repos/omero-ontop-mappings/hack24 ./run-ontop.sh
To leave the screen session press and hold CTRL, press and release a, press and release d, release CTRL. This brings you back into your login shell. You can then logout from the server, the screen session will continue in the background.
https://medium.com/wallscope/comparing-linked-data-triplestores-ebfac8c3ad4f A log of all benchmark runs executed during the 2024 de.NBI BioHackathon is in the logbook document.