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
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/ea432007 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/ea432007 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/ea432007 Branch: refs/heads/master Commit: ea4320079c79db73eb9bac3e7b73755bc6b2e57b Parents: 3c9d0a9 Author: Stian Soiland-Reyes <[email protected]> Authored: Thu May 10 18:17:19 2018 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Thu May 10 18:17:19 2018 +0100 ---------------------------------------------------------------------- .../robundle/manifest/RDFToManifest.java | 32 +++++++++++++++++--- .../src/main/resources/contexts/bundle.jsonld | 2 +- 2 files changed, 28 insertions(+), 6 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/ea432007/taverna-robundle/src/main/java/org/apache/taverna/robundle/manifest/RDFToManifest.java ---------------------------------------------------------------------- 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 @@ public class RDFToManifest { private OntClass standard; + private OntModel roterms; + + private ObjectProperty alternateOf; + public RDFToManifest() { loadOntologies(); } @@ -193,8 +197,26 @@ public class RDFToManifest { 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 @@ public class RDFToManifest { 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 @@ public class RDFToManifest { */ 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; http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/ea432007/taverna-robundle/src/main/resources/contexts/bundle.jsonld ---------------------------------------------------------------------- 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" },
