Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated WebserverCommand to use local ontologies if available #25

Merged
merged 3 commits into from
Oct 16, 2018
Merged

Updated WebserverCommand to use local ontologies if available #25

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
b6ee6c5
Updated WebserverCommand to use local ontologies if available.
gaurav Aug 27, 2018
1967d99
Updated CHANGELOG.md with changes to WebserverCommand.
gaurav Oct 8, 2018
ae5ba48
Merge branch 'master' into use_local_ontologies_in_webserver
gaurav Oct 8, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ Based on the suggestion at https://keepachangelog.com/en/1.0.0/.
- Removed Eclipse files that should not have been added in [phyloref/jphyloref#13].
- Moved code for determining Phyloref statuses to PhylorefHelper. This is part of
[phyloref/jphyloref#8].
- WebserverCommand now looks for ontologies in the local 'ontologies/' directory.

## 0.2 - 2018-06-20
- Added support for phyloreference statuses using the Publication Status Ontology
Expand Down
8 changes: 8 additions & 0 deletions src/main/java/org/phyloref/jphyloref/commands/WebserverCommand.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
import org.semanticweb.owlapi.rio.RioOWLRDFConsumerAdapter;
import org.semanticweb.owlapi.search.EntitySearcher;
import org.semanticweb.owlapi.util.AnonymousNodeChecker;
import org.semanticweb.owlapi.util.AutoIRIMapper;
import org.semanticweb.owlapi.util.VersionInfo;

import fi.iki.elonen.NanoHTTPD;
Expand Down Expand Up @@ -160,6 +161,13 @@ public JSONObject serveReason(File jsonldFile) throws OWLOntologyCreationExcepti

// Prepare an ontology to fill with the provided JSON-LD file.
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();

// Is purl.obolibrary.org down? No worries, you can access local copies
// of your ontologies in the 'ontologies/' folder.
AutoIRIMapper mapper = new AutoIRIMapper(new File("ontologies"), true);
System.err.println("Found local ontologies: " + mapper.getOntologyIRIs());
manager.addIRIMapper(mapper);

OWLOntology ontology = manager.createOntology();
OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration();

Expand Down