From 1c984b87cc8a8b8dcbafbbae7ae40337972369cd Mon Sep 17 00:00:00 2001 From: Pascal Christoph Date: Mon, 6 Nov 2023 09:00:55 +0100 Subject: [PATCH 1/4] Reenable test by getting monarch-context (#175) Storing monarch-context into this repo will make the tests more stable. --- .../github/jsonldjava/core/LocalBaseTest.java | 3 - .../test/resources/custom/base-0001-in.jsonld | 7 +- .../test/resources/custom/base-0002-in.jsonld | 7 +- .../resources/custom/monarch-context.jsonld | 149 ++++++++++++++++++ 4 files changed, 157 insertions(+), 9 deletions(-) create mode 100644 core/src/test/resources/custom/monarch-context.jsonld diff --git a/core/src/test/java/com/github/jsonldjava/core/LocalBaseTest.java b/core/src/test/java/com/github/jsonldjava/core/LocalBaseTest.java index e12c9a02..22093345 100644 --- a/core/src/test/java/com/github/jsonldjava/core/LocalBaseTest.java +++ b/core/src/test/java/com/github/jsonldjava/core/LocalBaseTest.java @@ -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 { @@ -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 { diff --git a/core/src/test/resources/custom/base-0001-in.jsonld b/core/src/test/resources/custom/base-0001-in.jsonld index f9bd58fd..12a082af 100644 --- a/core/src/test/resources/custom/base-0001-in.jsonld +++ b/core/src/test/resources/custom/base-0001-in.jsonld @@ -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/", @@ -13,4 +13,5 @@ "ex:name": "Jim", "ex:friendOf": "1234", "@type": "Person" -} \ No newline at end of file +} + diff --git a/core/src/test/resources/custom/base-0002-in.jsonld b/core/src/test/resources/custom/base-0002-in.jsonld index 4b2e3848..d533f432 100644 --- a/core/src/test/resources/custom/base-0002-in.jsonld +++ b/core/src/test/resources/custom/base-0002-in.jsonld @@ -1,5 +1,5 @@ { - "@context": [ + "@context": [ { "@base": "http://example.org/base/", "ex": "http://example.org/", @@ -7,10 +7,11 @@ "@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" -} \ No newline at end of file +} + diff --git a/core/src/test/resources/custom/monarch-context.jsonld b/core/src/test/resources/custom/monarch-context.jsonld new file mode 100644 index 00000000..472f4153 --- /dev/null +++ b/core/src/test/resources/custom/monarch-context.jsonld @@ -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_" + } +} From 156ec3e0f3325ed3abaa62e452d3d3610d7e7f53 Mon Sep 17 00:00:00 2001 From: Pascal Christoph Date: Mon, 6 Nov 2023 10:03:50 +0100 Subject: [PATCH 2/4] Update dependencies - bump Jackson version to 2.12.7.1 --- pom.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index f724db6b..f7662a72 100755 --- a/pom.xml +++ b/pom.xml @@ -42,6 +42,7 @@ 4.5.13 4.4.14 2.12.7 + 2.12.7.1 4.13.2 1.7.32 1.2.7 @@ -66,7 +67,7 @@ com.fasterxml.jackson.core jackson-databind - ${jackson.version} + ${jackson-databind.version} com.fasterxml.jackson.core From 1cff4ce3093bce405c52b7b52737e0982119b4a0 Mon Sep 17 00:00:00 2001 From: Pascal Christoph Date: Mon, 6 Nov 2023 10:08:44 +0100 Subject: [PATCH 3/4] Prepare for release Signed-off-by: christoph@hbz-nrw.de --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 6e354ba5..f1102e69 100644 --- a/README.md +++ b/README.md @@ -449,6 +449,10 @@ Alternatively, we can also host your repository in the jsonld-java organisation CHANGELOG ========= +### 2023-11-06 +* Release 0.13.6 +* Bump Jackson-databind version to latest for security update + ### 2023-11-03 * Release 0.13.5 * Bump Jackson and Guava versions to latest for security updates From 01c3086a2bba620bf74ac6440797275cb41cbe86 Mon Sep 17 00:00:00 2001 From: Pascal Christoph Date: Mon, 6 Nov 2023 10:16:20 +0100 Subject: [PATCH 4/4] Release 0.13.6 Signed-off-by: christoph@hbz-nrw.de --- core/pom.xml | 2 +- pom.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/core/pom.xml b/core/pom.xml index 12a00243..f14fb287 100755 --- a/core/pom.xml +++ b/core/pom.xml @@ -4,7 +4,7 @@ jsonld-java-parent com.github.jsonld-java - 0.13.6-SNAPSHOT + 0.13.6 4.0.0 jsonld-java diff --git a/pom.xml b/pom.xml index f7662a72..de5316fa 100755 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 com.github.jsonld-java jsonld-java-parent - 0.13.6-SNAPSHOT + 0.13.6 JSONLD Java :: Parent Json-LD Java Parent POM pom