TAVERNA-1046: Pick up ORCID from manifest
Note that this modifies our "cached" bundle.jsonld context
to map "orcid" alternatively to prov:alternateOf -- this is not
currently reflected upstream in https://w3id.org/bundle/context
diff --git a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
index c144f19..2976234 100644
--- a/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
+++ b/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java
@@ -163,6 +163,10 @@
private OntClass standard;
+ private OntModel roterms;
+
+ private ObjectProperty alternateOf;
+
public RDFToManifest() {
loadOntologies();
}
@@ -193,8 +197,26 @@
List<Agent> creators = new ArrayList<>();
for (Individual agent : listObjectProperties(in, property)) {
Agent a = new Agent();
- if (agent.getURI() != null)
- a.setUri(relativizeFromBase(agent.getURI(), base));
+
+ // Check for any ORCIDs, note that "orcid" is mapped as
+ // prov:alternateOf in our modified bundle.jsonld
+ for (Individual alternate : listObjectProperties(agent, alternateOf)) {
+ if (alternate.isURIResource() && (
+ alternate.getURI().startsWith("https://orcid.org/") ||
+ alternate.getURI().startsWith("http://orcid.org/"))) {
+ // TODO: Check against https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier
+ a.setOrcid(URI.create(alternate.getURI()));
+ break;
+ }
+ }
+ if (agent.isURIResource()) {
+ URI agentURI = relativizeFromBase(agent.getURI(), base);
+ if ("orcid.org".equals(agentURI.getHost()) && a.getOrcid() == null) {
+ a.setOrcid(agentURI);
+ } else {
+ a.setUri(agentURI);
+ }
+ }
RDFNode name = agent.getPropertyValue(foafName);
if (name != null && name.isLiteral())
@@ -366,8 +388,8 @@
if (prov != null)
return;
OntModel ontModel = loadOntologyFromClasspath(PROV_O_RDF, PROV_O);
-
- checkNotNull(ontModel);
+ alternateOf = ontModel.getObjectProperty(PROV + "alternateOf");
+ checkNotNull(ontModel, alternateOf);
prov = ontModel;
}
@@ -571,7 +593,7 @@
*/
for (Individual body : listObjectProperties(
model.getOntResource(ann), hasBody)) {
- if (body.getURI() == null) {
+ if (! body.isURIResource()) {
logger.warning("Can't find annotation body for anonymous "
+ body);
continue;
diff --git a/taverna-robundle/src/main/resources/contexts/bundle.jsonld b/taverna-robundle/src/main/resources/contexts/bundle.jsonld
index cadb9ff..170777f 100644
--- a/taverna-robundle/src/main/resources/contexts/bundle.jsonld
+++ b/taverna-robundle/src/main/resources/contexts/bundle.jsonld
@@ -88,7 +88,7 @@
"@id": "foaf:name"
},
"orcid": {
- "@id": "roterms:orcid",
+ "@id": "prov:alternateOf",
"@type": "@id"
},
