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Merged
dr0i merged 1 commit into from
Nov 6, 2023
Merged

Reenable test by getting monarch-contex #339

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3 changes: 0 additions & 3 deletions core/src/test/java/com/github/jsonldjava/core/LocalBaseTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,11 @@
import java.nio.charset.Charset;
import java.util.List;

import org.junit.Ignore;
import org.junit.Test;

import com.github.jsonldjava.utils.JsonUtils;

public class LocalBaseTest {
@Ignore("TODO: context does no more resolve - see https://github.com/jsonld-java/jsonld-java/issues/175")
@Test
public void testMixedLocalRemoteBaseRemoteContextFirst() throws Exception {

Expand All @@ -38,7 +36,6 @@ public void testMixedLocalRemoteBaseRemoteContextFirst() throws Exception {
assertEquals(expanded, output);
}

@Ignore("TODO: context does no more resolve - see https://github.com/jsonld-java/jsonld-java/issues/175")
@Test
public void testMixedLocalRemoteBaseLocalContextFirst() throws Exception {

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7 changes: 4 additions & 3 deletions core/src/test/resources/custom/base-0001-in.jsonld
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"@context": [
"https://raw.githubusercontent.com/monarch-initiative/monarch-app/master/conf/monarch-context.jsonld",
"@context": [
"https://raw.githubusercontent.com/jsonld-java/jsonld-java/master/core/src/test/resources/custom/monarch-context.jsonld",
{
"@base": "http://example.org/base/",
"ex": "http://example.org/",
Expand All @@ -13,4 +13,5 @@
"ex:name": "Jim",
"ex:friendOf": "1234",
"@type": "Person"
}
}

7 changes: 4 additions & 3 deletions core/src/test/resources/custom/base-0002-in.jsonld
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@@ -1,16 +1,17 @@
{
"@context": [
"@context": [
{
"@base": "http://example.org/base/",
"ex": "http://example.org/",
"ex:friendOf": {
"@type": "@id"
}
},
"https://raw.githubusercontent.com/monarch-initiative/monarch-app/master/conf/monarch-context.jsonld"
"https://raw.githubusercontent.com/jsonld-java/jsonld-java/master/core/src/test/resources/custom/monarch-context.jsonld"
],
"@id": "3456",
"ex:name": "Jim",
"ex:friendOf": "1234",
"@type": "Person"
}
}

149 changes: 149 additions & 0 deletions core/src/test/resources/custom/monarch-context.jsonld
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@@ -0,0 +1,149 @@
{
"@context" : {
"EFO" : "http://purl.obolibrary.org/obo/EFO_",
"obo" : "http://purl.obolibrary.org/obo/",
"inheritance" : "monarch:mode_of_inheritance",
"@base" : "http://monarch-initiative.org/",
"email" : "foaf:mbox",
"BIND" : "http://identifiers.org/bind/bind:",
"morpholino" : "GENO:0000417",
"GENO" : "http://purl.obolibrary.org/obo/GENO_",
"UMLS" : "http://purl.obolibrary.org/obo/UMLS_",
"dcat" : "http://www.w3.org/ns/dcat#",
"PMID" : "http://www.ncbi.nlm.nih.gov/pubmed/",
"MP" : "http://purl.obolibrary.org/obo/MP_",
"ISBN-10" : "http://monarch-initiative.org/publications/ISBN:",
"rdf" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"title" : "dc:title",
"Class" : "owl:Class",
"FBbt" : "http://purl.obolibrary.org/obo/FBbt_",
"pathway_associations" : "rdfs:seeAlso",
"FBInternalGT" : "http://monarchinitiative.org/genotype/",
"has_genotype" : "GENO:0000222",
"genotype" : "GENO:0000000",
"void" : "http://rdfs.org/ns/void#",
"has_phenotype" : "RO:0002200",
"reference_locus" : "GENO:0000036",
"dbVar" : "http://identifiers.org/dbVar_",
"AQTLTrait" : "http://purl.obolibrary.org/obo/AQTLTrait_",
"phenotype_associations" : "rdfs:seeAlso",
"ECO" : "http://purl.obolibrary.org/obo/ECO_",
"WB" : "http://identifiers.org/WormBase:",
"rdfs" : "http://www.w3.org/2000/01/rdf-schema#",
"variant_loci" : "GENO:0000027",
"MedGen" : "http://purl.obolibrary.org/obo/MedGen_",
"creator" : {
"@id" : "dc:creator",
"@type" : "@id"
},
"SIO" : "http://semanticscience.org/resource/SIO_",
"DOID" : "http://purl.obolibrary.org/obo/DOID_",
"Ensembl" : "http://identifiers.org/ensembl:",
"id" : "@id",
"publisher" : "dc:publisher",
"depiction" : {
"@id" : "foaf:depiction",
"@type" : "@id"
},
"ENSEMBL" : "http://identifiers.org/ensembl:",
"monarch" : "http://monarchinitiative.org/",
"ORPHANET" : "http://purl.obolibrary.org/obo/ORPHANET_",
"owl" : "http://www.w3.org/2002/07/owl#",
"GeneReviews" : "http://www.ncbi.nlm.nih.gov/books/",
"SNOMED_CT" : "http://purl.obolibrary.org/obo/SNOMED_",
"chromosomal_region" : "GENO:0000390",
"EOM" : "http://purl.obolibrary.org/obo/EOM_",
"type" : {
"@id" : "rdf:type",
"@type" : "@id"
},
"FlyBase" : "http://identifiers.org/flybase:",
"DECIPHER" : "http://purl.obolibrary.org/obo/DECIPHER_",
"faldo" : "http://biohackathon.org/resource/faldo#",
"prov" : "http://www.w3.org/ns/prov#",
"MIM" : "http://purl.obolibrary.org/obo/OMIM_",
"genomic_variation_complement" : "GENO:0000009",
"evidence" : "monarch:evidence",
"BioGRID" : "http://purl.obolibrary.org/BioGRID_",
"dcterms" : "http://purl.org/dc/terms/",
"sequence_alteration" : "SO:0001059",
"RO" : "http://purl.obolibrary.org/obo/RO_",
"created" : {
"@id" : "dc:created",
"@type" : "xsd:dateTime"
},
"Orphanet" : "http://purl.obolibrary.org/obo/ORPHANET_",
"oa" : "http://www.w3.org/ns/oa#",
"SGD" : "http://identifiers.org/mgd/sgd:",
"Gene" : "http://purl.obolibrary.org/obo/NCBIGene_",
"PomBase" : "http://identifiers.org/PomBase:",
"genotype_associations" : "rdfs:seeAlso",
"xsd" : "http://www.w3.org/2001/XMLSchema#",
"OMIABreed" : "http://purl.obolibrary.org/obo/OMIA_",
"TAIR" : "http://identifiers.org/mgd/tair:",
"oboInOwl" : "http://www.geneontology.org/formats/oboInOwl#",
"description" : "dc:description",
"disease" : "monarch:disease",
"OMIAPub" : "http://purl.obolibrary.org/obo/OMIAPub_",
"foaf" : "http://xmlns.com/foaf/0.1/",
"idot" : "http://identifiers.org/",
"subClassOf" : "owl:subClassOf",
"source" : "dc:source",
"keyword" : "dcat:keyword",
"onset" : "monarch:age_of_onset",
"genomic_background" : "GENO:0000010",
"dictyBase" : "http://identifiers.org/dictyBase:",
"OMIA" : "http://purl.obolibrary.org/obo/OMIA_",
"has_part" : "BFO:0000051",
"ClinVarVariant" : "http://identifiers.org/ClinVarVariant_",
"gene_locus" : "GENO:0000014",
"effective_genotype" : "GENO:0000525",
"VT" : "http://purl.obolibrary.org/obo/VT_",
"Association" : "SIO:000897",
"resource" : "monarch:nif-resource",
"KEGG" : "http://identifiers.org/kegg:",
"Annotation" : "oa:Annotation",
"FBdv" : "http://purl.obolibrary.org/obo/FBdv_",
"GeneID" : "http://purl.obolibrary.org/obo/NCBIGene_",
"has_background" : "GENO:0000010",
"BFO" : "http://purl.obolibrary.org/obo/BFO_",
"FB" : "http://identifiers.org/flybase:",
"frequency" : "monarch:frequency",
"ZP" : "http://purl.obolibrary.org/obo/ZP_",
"OMIM" : "http://purl.obolibrary.org/obo/OMIM_",
"MGI" : "http://identifiers.org/mgd/MGI:",
"dc" : "http://purl.org/dc/terms/",
"MONARCH" : "http://monarchinitiative.org/MONARCH_",
"ClinVarHaplotype" : "http://identifiers.org/ClinVarHaplotype_",
"homepage" : {
"@id" : "foaf:homepage",
"@type" : "@id"
},
"RGD" : "http://identifiers.org/mgd/rgd:",
"CORIELL" : "http://purl.obolibrary.org/obo/CORIELL_",
"label" : "rdfs:label",
"NCBIGene" : "http://purl.obolibrary.org/obo/NCBIGene_",
"intrinsic_genotype" : "GENO:0000000",
"FBcv" : "http://purl.obolibrary.org/obo/FBcv_",
"WBStrain" : "http://identifiers.org/WormBase:",
"sequence_alteration_collection" : "GENO:0000025",
"reference" : "dc:publication",
"zygosity" : "GENO:0000133",
"chromosome" : "GENO:0000323",
"WormBase" : "http://identifiers.org/WormBase:",
"HPRD" : "http://identifiers.org/hprd/hprd:",
"ClinVar" : "http://purl.obolibrary.org/obo/ClinVar_",
"ISBN-13" : "http://monarch-initiative.org/publications/ISBN:",
"extrinsic_genotype" : "GENO:0000524",
"NCBITaxon" : "http://purl.obolibrary.org/obo/NCBITaxon_",
"environment" : "GENO:0000099",
"variant_locus" : "GENO:0000481",
"comment" : "rdfs:comment",
"SO" : "http://purl.obolibrary.org/obo/SO_",
"phenotype" : "monarch:phenotype",
"ZFIN" : "http://identifiers.org/zfin:",
"HP" : "http://purl.obolibrary.org/obo/HP_",
"MESH" : "http://purl.obolibrary.org/obo/MESH_",
"dbSNP" : "http://identifiers.org/dbSNP_"
}
}