From f61097e776e8427e66617a5cb43f3f8176c31581 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 17:49:33 +0100 Subject: [PATCH 1/8] Format pom.xml --- pom.xml | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/pom.xml b/pom.xml index 7f3a0d8c..322a6d58 100644 --- a/pom.xml +++ b/pom.xml @@ -1,4 +1,6 @@ - + 4.0.0 uk.org.llgc simpleAnnotationStore @@ -36,9 +38,9 @@ ${jsf.version} - org.primefaces - primefaces - ${primefaces.version} + org.primefaces + primefaces + ${primefaces.version} org.apache.jena @@ -267,7 +269,9 @@ package - copy + + copy + @@ -287,7 +291,8 @@ 1.10.4 - + install node and npm install-node-and-npm @@ -311,9 +316,9 @@ - org.codehaus.mojo - exec-maven-plugin - 1.3.2 + org.codehaus.mojo + exec-maven-plugin + 1.3.2 npm run test (test) From fbfb73dc53492c37b176b55a84efca7cc5128d2f Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 17:51:21 +0100 Subject: [PATCH 2/8] Update Jetty to latest v9, reuse version property --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index 322a6d58..25c3de33 100644 --- a/pom.xml +++ b/pom.xml @@ -13,7 +13,7 @@ 2.2.15 7.0 - 9.4.29.v20200521 + 9.4.56.v20240826 @@ -226,7 +226,7 @@ org.eclipse.jetty jetty-maven-plugin - 9.4.30.v20200611 + ${jetty.version} 8888 @@ -244,7 +244,7 @@ org.eclipse.jetty apache-jstl - 9.4.29.v20200521 + ${jetty.version} org.apache.taglibs From 563b3849a46b152b0299c9f4a73699ae8f9030c2 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 17:57:29 +0100 Subject: [PATCH 3/8] Update Log4J to latest 2.x --- pom.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index 25c3de33..c63ae760 100644 --- a/pom.xml +++ b/pom.xml @@ -14,6 +14,7 @@ 2.2.15 7.0 9.4.56.v20240826 + 2.24.2 @@ -151,17 +152,17 @@ org.apache.logging.log4j log4j-api - 2.16.0 + ${log4j.version} org.apache.logging.log4j log4j-core - 2.16.0 + ${log4j.version} org.apache.logging.log4j log4j-slf4j-impl - 2.16.0 + ${log4j.version} org.apache.solr From d030800ea7622b8494442ccb2fccc9badaf59aac Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 17:59:51 +0100 Subject: [PATCH 4/8] Use NodeJS 23 with included npm --- package-lock.json | 67 +++++++++++++++++++++++++++++++---------------- pom.xml | 4 +-- 2 files changed, 47 insertions(+), 24 deletions(-) diff --git a/package-lock.json b/package-lock.json index 2b4b3681..1fafb40c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,106 +1,129 @@ { + "name": "SimpleAnnotationServer", + "lockfileVersion": 3, "requires": true, - "lockfileVersion": 1, - "dependencies": { - "balanced-match": { + "packages": { + "": { + "devDependencies": { + "jasmine": "^3.9.0" + } + }, + "node_modules/balanced-match": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz", "integrity": "sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==", "dev": true }, - "brace-expansion": { + "node_modules/brace-expansion": { "version": "1.1.11", "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==", "dev": true, - "requires": { + "dependencies": { "balanced-match": "^1.0.0", "concat-map": "0.0.1" } }, - "concat-map": { + "node_modules/concat-map": { "version": "0.0.1", "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz", "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=", "dev": true }, - "fs.realpath": { + "node_modules/fs.realpath": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz", "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=", "dev": true }, - "glob": { + "node_modules/glob": { "version": "7.2.0", "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.0.tgz", "integrity": "sha512-lmLf6gtyrPq8tTjSmrO94wBeQbFR3HbLHbuyD69wuyQkImp2hWqMGB47OX65FBkPffO641IP9jWa1z4ivqG26Q==", + "deprecated": "Glob versions prior to v9 are no longer supported", "dev": true, - "requires": { + "dependencies": { "fs.realpath": "^1.0.0", "inflight": "^1.0.4", "inherits": "2", "minimatch": "^3.0.4", "once": "^1.3.0", "path-is-absolute": "^1.0.0" + }, + "engines": { + "node": "*" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" } }, - "inflight": { + "node_modules/inflight": { "version": "1.0.6", "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz", "integrity": "sha1-Sb1jMdfQLQwJvJEKEHW6gWW1bfk=", + "deprecated": "This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful.", "dev": true, - "requires": { + "dependencies": { "once": "^1.3.0", "wrappy": "1" } }, - "inherits": { + "node_modules/inherits": { "version": "2.0.4", "resolved": "https://registry.npmjs.org/inherits/-/inherits-2.0.4.tgz", "integrity": "sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ==", "dev": true }, - "jasmine": { + "node_modules/jasmine": { "version": "3.9.0", "resolved": "https://registry.npmjs.org/jasmine/-/jasmine-3.9.0.tgz", "integrity": "sha512-JgtzteG7xnqZZ51fg7N2/wiQmXon09szkALcRMTgCMX4u/m17gVJFjObnvw5FXkZOWuweHPaPRVB6DI2uN0wVA==", "dev": true, - "requires": { + "dependencies": { "glob": "^7.1.6", "jasmine-core": "~3.9.0" + }, + "bin": { + "jasmine": "bin/jasmine.js" } }, - "jasmine-core": { + "node_modules/jasmine-core": { "version": "3.9.0", "resolved": "https://registry.npmjs.org/jasmine-core/-/jasmine-core-3.9.0.tgz", "integrity": "sha512-Tv3kVbPCGVrjsnHBZ38NsPU3sDOtNa0XmbG2baiyJqdb5/SPpDO6GVwJYtUryl6KB4q1Ssckwg612ES9Z0dreQ==", "dev": true }, - "minimatch": { + "node_modules/minimatch": { "version": "3.0.4", "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.0.4.tgz", "integrity": "sha512-yJHVQEhyqPLUTgt9B83PXu6W3rx4MvvHvSUvToogpwoGDOUQ+yDrR0HRot+yOCdCO7u4hX3pWft6kWBBcqh0UA==", "dev": true, - "requires": { + "dependencies": { "brace-expansion": "^1.1.7" + }, + "engines": { + "node": "*" } }, - "once": { + "node_modules/once": { "version": "1.4.0", "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz", "integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=", "dev": true, - "requires": { + "dependencies": { "wrappy": "1" } }, - "path-is-absolute": { + "node_modules/path-is-absolute": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/path-is-absolute/-/path-is-absolute-1.0.1.tgz", "integrity": "sha1-F0uSaHNVNP+8es5r9TpanhtcX18=", - "dev": true + "dev": true, + "engines": { + "node": ">=0.10.0" + } }, - "wrappy": { + "node_modules/wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", diff --git a/pom.xml b/pom.xml index c63ae760..e6af82b3 100644 --- a/pom.xml +++ b/pom.xml @@ -300,8 +300,8 @@ generate-resources - v14.15.1 - 6.14.8 + v23.3.0 + From e9acec5612d183418bafbd867eb5c49402bdfc0a Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 18:19:34 +0100 Subject: [PATCH 5/8] Add jakarta.annotations, refactor javax.annotation references --- pom.xml | 5 +++++ .../store/controllers/AuthorisationController.java | 2 +- .../org/llgc/annotation/store/controllers/StatsService.java | 2 +- .../org/llgc/annotation/store/controllers/StoreService.java | 2 +- .../org/llgc/annotation/store/controllers/UserService.java | 2 +- 5 files changed, 9 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index e6af82b3..b8fec86d 100644 --- a/pom.xml +++ b/pom.xml @@ -68,6 +68,11 @@ --> + + jakarta.annotation + jakarta.annotation-api + 3.0.0 + commons-codec commons-codec diff --git a/src/main/java/uk/org/llgc/annotation/store/controllers/AuthorisationController.java b/src/main/java/uk/org/llgc/annotation/store/controllers/AuthorisationController.java index f42b52dd..b1cfa021 100644 --- a/src/main/java/uk/org/llgc/annotation/store/controllers/AuthorisationController.java +++ b/src/main/java/uk/org/llgc/annotation/store/controllers/AuthorisationController.java @@ -2,7 +2,7 @@ import javax.faces.bean.ManagedBean; import javax.faces.bean.RequestScoped; -import javax.annotation.PostConstruct; +import jakarta.annotation.PostConstruct; import javax.faces.context.FacesContext; diff --git a/src/main/java/uk/org/llgc/annotation/store/controllers/StatsService.java b/src/main/java/uk/org/llgc/annotation/store/controllers/StatsService.java index 247f27a2..5ffc9b35 100644 --- a/src/main/java/uk/org/llgc/annotation/store/controllers/StatsService.java +++ b/src/main/java/uk/org/llgc/annotation/store/controllers/StatsService.java @@ -2,7 +2,7 @@ import javax.faces.bean.ManagedBean; import javax.faces.bean.RequestScoped; -import javax.annotation.PostConstruct; +import jakarta.annotation.PostConstruct; import org.primefaces.model.chart.BarChartModel; import org.primefaces.model.chart.PieChartModel; diff --git a/src/main/java/uk/org/llgc/annotation/store/controllers/StoreService.java b/src/main/java/uk/org/llgc/annotation/store/controllers/StoreService.java index de616ab2..3edebc1c 100644 --- a/src/main/java/uk/org/llgc/annotation/store/controllers/StoreService.java +++ b/src/main/java/uk/org/llgc/annotation/store/controllers/StoreService.java @@ -2,7 +2,7 @@ import javax.faces.bean.ManagedBean; import javax.faces.bean.ApplicationScoped; -import javax.annotation.PostConstruct; +import jakarta.annotation.PostConstruct; import uk.org.llgc.annotation.store.data.PageAnnoCount; import uk.org.llgc.annotation.store.data.Manifest; diff --git a/src/main/java/uk/org/llgc/annotation/store/controllers/UserService.java b/src/main/java/uk/org/llgc/annotation/store/controllers/UserService.java index cb36bd3c..98db2462 100644 --- a/src/main/java/uk/org/llgc/annotation/store/controllers/UserService.java +++ b/src/main/java/uk/org/llgc/annotation/store/controllers/UserService.java @@ -2,7 +2,7 @@ import javax.faces.bean.ManagedBean; import javax.faces.bean.RequestScoped; -import javax.annotation.PostConstruct; +import jakarta.annotation.PostConstruct; import javax.faces.context.FacesContext; From e6eb837f51060ac7e8f0e80352e2330edfffc018 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 18:21:26 +0100 Subject: [PATCH 6/8] Update Jena, refactor use of QueryEngineHTTP to QueryExecutionHTTP --- pom.xml | 13 +++++-------- .../store/adapters/rdf/sesame/SesameStore.java | 4 ++-- 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/pom.xml b/pom.xml index b8fec86d..8c5d53b3 100644 --- a/pom.xml +++ b/pom.xml @@ -43,29 +43,26 @@ primefaces ${primefaces.version} - + + org.apache.jena jena-tdb - 4.3.1 + 4.10.0 org.apache.jena jena-arq - 4.3.1 + 4.10.0 org.apache.jena jena-shaded-guava - diff --git a/src/main/java/uk/org/llgc/annotation/store/adapters/rdf/sesame/SesameStore.java b/src/main/java/uk/org/llgc/annotation/store/adapters/rdf/sesame/SesameStore.java index 13950cf3..faf06312 100644 --- a/src/main/java/uk/org/llgc/annotation/store/adapters/rdf/sesame/SesameStore.java +++ b/src/main/java/uk/org/llgc/annotation/store/adapters/rdf/sesame/SesameStore.java @@ -10,7 +10,7 @@ import org.apache.jena.query.QueryFactory; import org.apache.jena.query.QueryExecutionFactory; import org.apache.jena.query.QueryExecution; -import org.apache.jena.sparql.engine.http.QueryEngineHTTP; +import org.apache.jena.sparql.exec.http.QueryExecutionHTTP; import org.apache.jena.query.ParameterizedSparqlString; import org.apache.jena.query.Syntax; @@ -251,7 +251,7 @@ protected String indexManifestOnly(final String pShortId, Map pMa protected QueryExecution getQueryExe(final String pQuery) { - return new QueryEngineHTTP(((HTTPRepository)_repo).getRepositoryURL(),pQuery); + return QueryExecutionHTTP.service(((HTTPRepository)_repo).getRepositoryURL(), pQuery); } protected Resource createIRI(final String pURI) { From 49c31b95034bf8f127320f0af8bc133eb5b0b407 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Thu, 5 Dec 2024 18:42:25 +0100 Subject: [PATCH 7/8] Update various dependencies, add exclusions Commons logging was found in multiple (transitive) dependencies. --- pom.xml | 48 +++++++++++++++++++++++++++++++++--------------- 1 file changed, 33 insertions(+), 15 deletions(-) diff --git a/pom.xml b/pom.xml index 8c5d53b3..98b121fe 100644 --- a/pom.xml +++ b/pom.xml @@ -73,17 +73,17 @@ commons-codec commons-codec - 1.15 + 1.17.1 - commons-fileupload - commons-fileupload - 1.4 + commons-fileupload + commons-fileupload + 1.5 com.github.jsonld-java jsonld-java - 0.13.4 + 0.13.6 org.apache.httpcomponents @@ -103,7 +103,7 @@ jaxen jaxen - 1.2.0 + 2.0.0 org.jdom @@ -113,12 +113,12 @@ com.fasterxml.jackson.core jackson-core - 2.13.0 + 2.18.2 com.fasterxml.jackson.core jackson-databind - 2.13.0 + 2.18.2 org.openrdf.sesame @@ -133,7 +133,7 @@ org.apache.httpcomponents httpclient - 4.5.13 + 4.5.14 commons-logging @@ -176,17 +176,29 @@ org.elasticsearch.client elasticsearch-rest-high-level-client 7.13.4 + + + commons-logging + commons-logging + + com.amazonaws aws-java-sdk-core - 1.12.129 + 1.12.779 + + + commons-logging + commons-logging + + - org.mockito - mockito-core - 4.1.0 + org.mockito + mockito-core + 5.14.2 test @@ -199,12 +211,18 @@ com.github.scribejava scribejava-apis - 8.3.1 + 8.3.3 org.springframework.security spring-security-core - 5.6.0 + 6.4.1 + + + org.springframework + spring-jcl + + From 8c4eaca1e7a7b182d64069709c6990ecece8d168 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Mon, 9 Dec 2024 14:12:31 +0100 Subject: [PATCH 8/8] Revert Spring Security dependency to latest 5.x.y --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 98b121fe..56a21179 100644 --- a/pom.xml +++ b/pom.xml @@ -216,7 +216,7 @@ org.springframework.security spring-security-core - 6.4.1 + 5.8.16 org.springframework