New upstream version 0.13.6

629305fe · Andrius Merkys · 92350c75 · 629305fe · 629305fe · 629305fe
Commit 629305fe authored 1 year ago by Andrius Merkys
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ From Maven
    <dependency>
        <groupId>com.github.jsonld-java</groupId>
        <artifactId>jsonld-java</artifactId>
-        <version>0.13.4</version>
+        <version>0.13.5</version>
    </dependency>

 Code example
@@ -323,11 +323,11 @@ Here is the basic outline for what your module's pom.xml should look like
  <parent>
    <groupId>com.github.jsonld-java</groupId>
    <artifactId>jsonld-java-parent</artifactId>
-    <version>0.13.4</version>
+    <version>0.13.5</version>
  </parent>
  <modelVersion>4.0.0</modelVersion>
  <artifactId>jsonld-java-{your module}</artifactId>
-  <version>0.13.4-SNAPSHOT</version>
+  <version>0.13.5-SNAPSHOT</version>
  <name>JSONLD Java :: {your module name}</name>
  <description>JSON-LD Java integration module for {RDF Library your module integrates}</description>
  <packaging>jar</packaging>
@@ -449,6 +449,14 @@ 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
+
 ### 2021-12-13
 * Release 0.13.4
 * Switch test logging from log4j to logback (Patch by @ansell)

--- a/core/pom.xml
+++ b/core/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>jsonld-java-parent</artifactId>
 		<groupId>com.github.jsonld-java</groupId>
-		<version>0.13.4</version>
+		<version>0.13.6</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>jsonld-java</artifactId>

--- a/core/src/test/resources/custom/base-0001-in.jsonld
+++ b/core/src/test/resources/custom/base-0001-in.jsonld
 {
-    "@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
+}
+
--- a/core/src/test/resources/custom/base-0002-in.jsonld
+++ b/core/src/test/resources/custom/base-0002-in.jsonld
 {
-    "@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
+}
+
--- a/core/src/test/resources/custom/monarch-context.jsonld
+++ b/core/src/test/resources/custom/monarch-context.jsonld
+{
+   "@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_"
+   }
+}
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>com.github.jsonld-java</groupId>
 	<artifactId>jsonld-java-parent</artifactId>
-	<version>0.13.4</version>
+	<version>0.13.6</version>
 	<name>JSONLD Java :: Parent</name>
 	<description>Json-LD Java Parent POM</description>
 	<packaging>pom</packaging>
@@ -41,7 +41,8 @@

 		<httpclient.version>4.5.13</httpclient.version>
 		<httpcore.version>4.4.14</httpcore.version>
-		<jackson.version>2.11.4</jackson.version>
+		<jackson.version>2.12.7</jackson.version>
+		<jackson-databind.version>2.12.7.1</jackson-databind.version>
 		<junit.version>4.13.2</junit.version>
 		<slf4j.version>1.7.32</slf4j.version>
 		<logback.version>1.2.7</logback.version>
@@ -66,7 +67,7 @@
 			<dependency>
 				<groupId>com.fasterxml.jackson.core</groupId>
 				<artifactId>jackson-databind</artifactId>
-				<version>${jackson.version}</version>
+				<version>${jackson-databind.version}</version>
 			</dependency>
 			<dependency>
 				<groupId>com.fasterxml.jackson.core</groupId>
@@ -211,7 +212,7 @@
 			<dependency>
 				<groupId>com.google.guava</groupId>
 				<artifactId>guava</artifactId>
-				<version>29.0-jre</version>
+				<version>32.1.3-jre</version>
 			</dependency>
 		</dependencies>
 	</dependencyManagement>