Skip to content

Commit

Permalink
Added ability of JPhyloRef to load the context from resources.
Browse files Browse the repository at this point in the history
  • Loading branch information
@gaurav
gaurav committed Mar 26, 2024
1 parent ef9f231 commit 3639ff5
Show file tree
Hide file tree
Showing 3 changed files with 330 additions and 0 deletions.
41 changes: 41 additions & 0 deletions src/main/java/org/phyloref/jphyloref/helpers/JSONLDHelper.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,11 @@
import com.github.jsonldjava.core.DocumentLoader;
import com.github.jsonldjava.core.JsonLdError;
import com.github.jsonldjava.core.RemoteDocument;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.stream.Collectors;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.RDFParser;
import org.eclipse.rdf4j.rio.Rio;
Expand Down Expand Up @@ -74,6 +79,42 @@ public boolean isAnonymousNode(IRI iri) {
parser.set(
JSONLDSettings.DOCUMENT_LOADER,
new DocumentLoader() {
{
// Load built-in context files as injected documents.
try {
this.addInjectedDoc(
"https://ww.phyloref.org/phyx.js/context/v1.0.0/phyx.json",
loadResourceFileAsString("context/phyx-context-v1.0.0.json"));
} catch (IOException e) {
logger.error("Could not load Phyx context v1.0.0: " + e);
}

try {
this.addInjectedDoc(
"https://www.phyloref.org/phyx.js/context/v1.1.0/phyx.json",
loadResourceFileAsString("context/phyx-context-v1.1.0.json"));
} catch (IOException e) {
logger.error("Could not load Phyx context v1.1.0: " + e);
}
}

/**
* Load a text Resource as a String. Based on the code at
* https://stackoverflow.com/a/46613809/27310
*
* @return A String representation of the Resource specified.
*/
private String loadResourceFileAsString(String fileName) throws IOException {
ClassLoader classLoader = ClassLoader.getSystemClassLoader();
try (InputStream is = classLoader.getResourceAsStream(fileName)) {
if (is == null) throw new IOException("Could not find resource: " + fileName);
try (InputStreamReader isr = new InputStreamReader(is);
BufferedReader reader = new BufferedReader(isr)) {
return reader.lines().collect(Collectors.joining(System.lineSeparator()));
}
}
}

@Override
public RemoteDocument loadDocument(String url) throws JsonLdError {
try {
Expand Down
143 changes: 143 additions & 0 deletions src/main/resources/context/phyx-context-v1.0.0.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,143 @@
{
"@context": {
"xsd": "http://www.w3.org/2001/XMLSchema#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"owl": "http://www.w3.org/2002/07/owl#",
"skos": "http://www.w3.org/2004/02/skos/core#",
"obo": "http://purl.obolibrary.org/obo/",
"dwc": "http://rs.tdwg.org/dwc/terms/",
"dct": "http://purl.org/dc/terms/",
"tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
"tn": "http://rs.tdwg.org/ontology/voc/TaxonName#",
"testcase": "http://vocab.phyloref.org/phyloref/testcase.owl#",
"pso": "http://purl.org/spar/pso/",
"tvc": "http://www.essepuntato.it/2012/04/tvc/",
"timeinterval": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#",
"phyloref": "http://ontology.phyloref.org/phyloref.owl#",
"opentree": "http://purl.org/opentree/nexson#",
"subClasses": {
"@reverse": "rdfs:subClassOf"
},
"label": {
"@id": "rdfs:label",
"@type": "xsd:string"
},
"labels": {
"@id": "rdfs:label",
"@type": "xsd:string",
"@container": "@set"
},
"namePublishedIn": "dwc:namePublishedIn",
"definitionSource": "obo:IAO_0000119",
"definition": {
"@id": "obo:IAO_0000115",
"@type": "xsd:string"
},
"hasName": {
"@id": "tc:hasName",
"@type": "tn:TaxonName"
},
"nameComplete": {
"@id": "tn:nameComplete",
"@type": "xsd:string"
},
"nomenclaturalCode": {
"@id": "tn:nomenclaturalCode",
"@type": "@id"
},
"scientificName": {
"@id": "dwc:scientificName",
"@type": "xsd:string"
},
"genusPart": {
"@id": "tn:genusPart",
"@type": "xsd:string"
},
"specificEpithet": {
"@id": "tn:specificEpithet",
"@type": "xsd:string"
},
"basisOfRecord": "dwc:basisOfRecord",
"occurrenceID": "dwc:occurrenceID",
"catalogNumber": "dwc:catalogNumber",
"collectionCode": "dwc:collectionCode",
"institutionCode": "dwc:institutionCode",
"subClassOf": {
"@id": "rdfs:subClassOf",
"@type": "@id"
},
"parent": {
"@id": "obo:CDAO_0000179",
"@type": "@id"
},
"children": {
"@id": "obo:CDAO_0000149",
"@type": "@id"
},
"siblings": {
"@id": "phyloref:has_Sibling",
"@type": "@id"
},
"owl:imports": {
"@id": "owl:imports",
"@type": "@id"
},
"equivalentClass": "owl:equivalentClass",
"intersectionOf": {
"@id": "owl:intersectionOf",
"@container": "@list"
},
"onProperty": {
"@id": "owl:onProperty",
"@type": "@id"
},
"someValuesFrom": {
"@id": "owl:someValuesFrom",
"@container": "@set"
},
"unionOf": {
"@id": "owl:unionOf",
"@container": "@list"
},
"hasValue": {
"@id": "owl:hasValue",
"@type": "xsd:string"
},
"nodes": {
"@reverse": "obo:CDAO_0000200",
"@container": "@set"
},
"hasRootNode": {
"@id": "obo:CDAO_0000148",
"@type": "@id"
},
"newick": {
"@id": "phyloref:newick_expression",
"@type": "xsd:string"
},
"curator": {
"@id": "opentree:curatorName",
"@type": "xsd:string"
},
"scientificNameAuthorship": {
"@id": "dwc:scientificNameAuthorship",
"@type": "xsd:string"
},
"nameAccordingTo": "tc:accordingTo",
"phylogenies": {
"@reverse": "rdfs:isDefinedBy",
"@container": "@set"
},
"phylorefs": {
"@reverse": "rdfs:isDefinedBy",
"@container": "@set"
},
"title": "dct:title",
"source": "dct:source",
"bibliographicCitation": "dct:bibliographicCitation",
"doi": "http://prismstandard.org/namespaces/basic/2.0/doi",
"representsTaxonomicUnits": "obo:CDAO_0000187",
"apomorphy": "phyloref:apomorphy"
}
}
146 changes: 146 additions & 0 deletions src/main/resources/context/phyx-context-v1.1.0.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,146 @@
{
"@context": {
"xsd": "http://www.w3.org/2001/XMLSchema#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"owl": "http://www.w3.org/2002/07/owl#",
"skos": "http://www.w3.org/2004/02/skos/core#",
"obo": "http://purl.obolibrary.org/obo/",
"dwc": "http://rs.tdwg.org/dwc/terms/",
"dct": "http://purl.org/dc/terms/",
"tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
"tn": "http://rs.tdwg.org/ontology/voc/TaxonName#",
"pso": "http://purl.org/spar/pso/",
"tvc": "http://www.essepuntato.it/2012/04/tvc/",
"timeinterval": "http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#",
"phyloref": "http://ontology.phyloref.org/phyloref.owl#",
"subClasses": {
"@reverse": "rdfs:subClassOf"
},
"label": {
"@id": "rdfs:label",
"@type": "xsd:string"
},
"labels": {
"@id": "rdfs:label",
"@type": "xsd:string",
"@container": "@set"
},
"namePublishedIn": "dwc:namePublishedIn",
"definitionSource": "obo:IAO_0000119",
"definition": {
"@id": "obo:IAO_0000115",
"@type": "xsd:string"
},
"hasName": {
"@id": "tc:hasName",
"@type": "tn:TaxonName"
},
"nameComplete": {
"@id": "tn:nameComplete",
"@type": "xsd:string"
},
"nomenclaturalCode": {
"@id": "tn:nomenclaturalCode",
"@type": "@id"
},
"scientificName": {
"@id": "dwc:scientificName",
"@type": "xsd:string"
},
"genusPart": {
"@id": "tn:genusPart",
"@type": "xsd:string"
},
"specificEpithet": {
"@id": "tn:specificEpithet",
"@type": "xsd:string"
},
"basisOfRecord": "dwc:basisOfRecord",
"occurrenceID": "dwc:occurrenceID",
"catalogNumber": "dwc:catalogNumber",
"collectionCode": "dwc:collectionCode",
"institutionCode": "dwc:institutionCode",
"subClassOf": {
"@id": "rdfs:subClassOf",
"@type": "@id"
},
"parent": {
"@id": "obo:CDAO_0000179",
"@type": "@id"
},
"children": {
"@id": "obo:CDAO_0000149",
"@type": "@id"
},
"siblings": {
"@id": "phyloref:has_Sibling",
"@type": "@id"
},
"owl:imports": {
"@id": "owl:imports",
"@type": "@id"
},
"equivalentClass": "owl:equivalentClass",
"intersectionOf": {
"@id": "owl:intersectionOf",
"@container": "@list"
},
"onProperty": {
"@id": "owl:onProperty",
"@type": "@id"
},
"someValuesFrom": {
"@id": "owl:someValuesFrom",
"@container": "@set"
},
"unionOf": {
"@id": "owl:unionOf",
"@container": "@list"
},
"hasValue": {
"@id": "owl:hasValue",
"@type": "xsd:string"
},
"nodes": {
"@reverse": "obo:CDAO_0000200",
"@container": "@set"
},
"hasRootNode": {
"@id": "obo:CDAO_0000148",
"@type": "@id"
},
"newick": {
"@id": "phyloref:newick_expression",
"@type": "xsd:string"
},
"curatorNotes": {
"@id": "obo:IAO_0000232",
"@type": "xsd:string"
},
"scientificNameAuthorship": {
"@id": "dwc:scientificNameAuthorship",
"@type": "xsd:string"
},
"nameAccordingTo": "tc:accordingTo",
"phylogenies": {
"@reverse": "rdfs:isDefinedBy",
"@container": "@set"
},
"phylorefs": {
"@reverse": "rdfs:isDefinedBy",
"@container": "@set"
},
"title": "dct:title",
"source": "dct:source",
"bibliographicCitation": "dct:bibliographicCitation",
"doi": "http://prismstandard.org/namespaces/basic/2.0/doi",
"representsTaxonomicUnits": "obo:CDAO_0000187",
"apomorphy": "phyloref:apomorphy",
"contributors": {
"@id": "http://purl.org/dc/terms/contributor",
"@container": "@set"
},
"name": "http://xmlns.com/foaf/0.1/name"
}
}

0 comments on commit 3639ff5

Please sign in to comment.