Fix dependendency issues with commons logging (#11403)

* Fix dependendency issues with commons logging

update gemfx
update unirest to 4.x

* try again with logging module stuff

* remove commons logging from merged module agian

* fix transitive circular dep stuff

* cleanup , fix urls

* remove imports

* reset config

* fix spacing

* replace quotes

build.gradle

@@ -165,6 +165,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.11.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
+    implementation 'commons-logging:commons-logging:1.3.2'
     implementation 'com.h2database:h2-mvstore:2.2.224'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
@@ -222,9 +223,11 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.25.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.32.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
+        exclude group: 'org.apache.commons.validator'
+        exclude group: 'org.apache.commons.commons-logging'
         exclude group: 'org.openjfx'
         exclude group: 'org.apache.logging.log4j'
         exclude group: 'tech.units'
@@ -235,12 +238,14 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.2.1'
 
     implementation 'org.jsoup:jsoup:1.17.2'
-    implementation 'com.konghq:unirest-java:3.14.5'
+    implementation 'com.konghq:unirest-java-core:4.4.0'
+    implementation 'com.konghq:unirest-modules-gson:4.4.0'
+    implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
 
     implementation 'org.slf4j:slf4j-api:2.0.13'
-    implementation "org.tinylog:tinylog-api:2.7.0"
-    implementation "org.tinylog:slf4j-tinylog:2.7.0"
-    implementation "org.tinylog:tinylog-impl:2.7.0"
+    implementation 'org.tinylog:tinylog-api:2.7.0'
+    implementation 'org.tinylog:slf4j-tinylog:2.7.0'
+    implementation 'org.tinylog:tinylog-impl:2.7.0'
 
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.13'
@@ -532,7 +537,7 @@ testlogger {
     showStackTraces false
 }
 
-tasks.withType(Test) {
+tasks.withType(Test).configureEach {
     reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
     // Enable parallel tests (on desktop).
     // See https://docs.gradle.org/8.1/userguide/performance.html#execute_tests_in_parallel for details.
@@ -672,7 +677,7 @@ jlink {
     // but it was removed in the newer releases.
     // The pom.xml associated with such a non-modular artifact does not mention that the artifact depends on the removed code
     // (because the artifact was published when this code was still available in the JDK).
-    forceMerge "controlsfx", "bcprov", "jaxb", "istack", "stax", "log4j"
+    forceMerge "controlsfx", "bcprov", "jaxb", "istack", "stax"
 
     // TODO: Remove the following correction to the merged module
     // The module descriptor automatically generated by the plugin for the merged module contained some invalid entries.
@@ -712,12 +717,14 @@ jlink {
         requires 'jakarta.xml.bind'
         requires 'org.apache.commons.lang3'
         requires 'org.apache.commons.text'
+        requires 'org.apache.commons.logging';
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
         uses 'org.mariadb.jdbc.LocalInfileInterceptor'
         uses 'org.eclipse.jgit.transport.SshSessionFactory'
         uses 'org.eclipse.jgit.lib.GpgSigner'
+        uses 'kong.unirest.core.json.JsonEngine';
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'
         provides 'org.mariadb.jdbc.authentication.AuthenticationPlugin' with 'org.mariadb.jdbc.internal.com.send.authentication.CachingSha2PasswordPlugin',
@@ -733,6 +740,8 @@ jlink {
                 'org.mariadb.jdbc.credential.system.PropertiesCredentialPlugin'
         provides 'java.security.Provider' with 'org.bouncycastle.jce.provider.BouncyCastleProvider',
                 'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'
+        provides 'kong.unirest.core.json.JsonEngine' with 'kong.unirest.modules.gson.GsonEngine';
+
     }
 
     jpackage {

src/main/java/module-info.java

@@ -78,8 +78,8 @@
     requires org.glassfish.hk2.api;
 
     // http clients
-    requires unirest.java;
-    requires org.apache.httpcomponents.httpclient;
+    requires unirest.java.core;
+    requires unirest.modules.gson;
     requires org.jsoup;
 
     // SQL databases
@@ -97,6 +97,7 @@
     requires org.apache.commons.io;
     requires org.apache.commons.lang3;
     requires org.apache.commons.text;
+    requires org.apache.commons.logging;
 
     requires com.github.tomtung.latex2unicode;
     requires fastparse;
@@ -148,4 +149,5 @@
     requires de.saxsys.mvvmfx.validation;
     requires dd.plist;
     requires mslinks;
+    requires org.apache.httpcomponents.core5.httpcore5;
 }

src/main/java/org/jabref/gui/JabRefGUI.java

@@ -41,7 +41,7 @@
 
 import com.airhacks.afterburner.injection.Injector;
 import com.tobiasdiez.easybind.EasyBind;
-import kong.unirest.Unirest;
+import kong.unirest.core.Unirest;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/gui/entryeditor/SciteTabViewModel.java

@@ -23,7 +23,7 @@
 import org.jabref.model.entry.identifier.DOI;
 import org.jabref.preferences.PreferencesService;
 
-import kong.unirest.json.JSONObject;
+import kong.unirest.core.json.JSONObject;
 import org.tinylog.Logger;
 
 public class SciteTabViewModel extends AbstractViewModel {

src/main/java/org/jabref/gui/entryeditor/SciteTallyModel.java

@@ -1,6 +1,6 @@
 package org.jabref.gui.entryeditor;
 
-import kong.unirest.json.JSONObject;
+import kong.unirest.core.json.JSONObject;
 
 /**
  * Simple model object to hold the scite.ai tallies data for a given DOI

src/main/java/org/jabref/gui/errorconsole/ErrorConsoleViewModel.java

@@ -22,7 +22,7 @@
 import org.jabref.preferences.PreferencesService;
 
 import com.tobiasdiez.easybind.EasyBind;
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java

@@ -43,7 +43,7 @@
 import org.jabref.preferences.FilePreferences;
 
 import com.tobiasdiez.easybind.EasyBind;
-import kong.unirest.UnirestException;
+import kong.unirest.core.UnirestException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/gui/preferences/network/NetworkTabViewModel.java

@@ -38,7 +38,7 @@
 import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
 import de.saxsys.mvvmfx.utils.validation.ValidationStatus;
 import de.saxsys.mvvmfx.utils.validation.Validator;
-import kong.unirest.UnirestException;
+import kong.unirest.core.UnirestException;
 
 public class NetworkTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty versionCheckProperty = new SimpleBooleanProperty();

src/main/java/org/jabref/gui/preferences/websearch/WebSearchTabViewModel.java

@@ -39,7 +39,7 @@
 import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.PreferencesService;
 
-import kong.unirest.UnirestException;
+import kong.unirest.core.UnirestException;
 
 public class WebSearchTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty enableWebSearchProperty = new SimpleBooleanProperty();

src/main/java/org/jabref/logic/importer/fetcher/ACMPortalFetcher.java

@@ -14,7 +14,7 @@
 import org.jabref.logic.importer.fetcher.transformers.DefaultQueryTransformer;
 import org.jabref.logic.importer.fileformat.ACMPortalParser;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 public class ACMPortalFetcher implements SearchBasedParserFetcher {

src/main/java/org/jabref/logic/importer/fetcher/ApsFetcher.java

@@ -12,7 +12,7 @@
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.identifier.DOI;
 
-import kong.unirest.Unirest;
+import kong.unirest.core.Unirest;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/importer/fetcher/ArXivFetcher.java

@@ -47,7 +47,7 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.OptionalUtil;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java

@@ -38,10 +38,10 @@
 import org.jabref.model.paging.Page;
 import org.jabref.model.strings.StringUtil;
 
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONException;
-import kong.unirest.json.JSONObject;
-import org.apache.http.client.utils.URIBuilder;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONException;
+import kong.unirest.core.json.JSONObject;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 /**

src/main/java/org/jabref/logic/importer/fetcher/BiodiversityLibrary.java

@@ -24,10 +24,10 @@
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.types.StandardEntryType;
 
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONException;
-import kong.unirest.json.JSONObject;
-import org.apache.http.client.utils.URIBuilder;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONException;
+import kong.unirest.core.json.JSONObject;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.tinylog.Logger;
 

src/main/java/org/jabref/logic/importer/fetcher/BvbFetcher.java

@@ -11,7 +11,7 @@
 import org.jabref.logic.importer.fetcher.transformers.DefaultQueryTransformer;
 import org.jabref.logic.importer.fileformat.MarcXmlParser;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 public class BvbFetcher implements SearchBasedParserFetcher {

src/main/java/org/jabref/logic/importer/fetcher/CiteSeer.java

@@ -16,10 +16,10 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
 
-import kong.unirest.JsonNode;
-import kong.unirest.Unirest;
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONElement;
+import kong.unirest.core.JsonNode;
+import kong.unirest.core.Unirest;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONElement;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 public class CiteSeer implements SearchBasedFetcher, FulltextFetcher {

src/main/java/org/jabref/logic/importer/fetcher/CollectionOfComputerScienceBibliographiesFetcher.java

@@ -21,7 +21,7 @@
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.field.UnknownField;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 public class CollectionOfComputerScienceBibliographiesFetcher implements SearchBasedParserFetcher {

src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java

@@ -31,10 +31,10 @@
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.model.util.OptionalUtil;
 
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONException;
-import kong.unirest.json.JSONObject;
-import org.apache.http.client.utils.URIBuilder;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONException;
+import kong.unirest.core.json.JSONObject;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 /**

src/main/java/org/jabref/logic/importer/fetcher/DBLPFetcher.java

@@ -23,7 +23,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 /**

src/main/java/org/jabref/logic/importer/fetcher/DOABFetcher.java

@@ -20,10 +20,10 @@
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.model.strings.StringUtil;
 
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONException;
-import kong.unirest.json.JSONObject;
-import org.apache.http.client.utils.URIBuilder;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONException;
+import kong.unirest.core.json.JSONObject;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 /**

src/main/java/org/jabref/logic/importer/fetcher/DOAJFetcher.java

@@ -24,9 +24,9 @@
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.model.strings.StringUtil;
 
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONObject;
-import org.apache.http.client.utils.URIBuilder;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONObject;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/jabref/logic/importer/fetcher/DiVA.java

@@ -12,7 +12,7 @@
 import org.jabref.logic.importer.Parser;
 import org.jabref.logic.importer.fileformat.BibtexParser;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 
 /*
  * http://www.diva-portal.org/smash/aboutdiva.jsf?dswid=-3222

src/main/java/org/jabref/logic/importer/fetcher/DoiFetcher.java

@@ -32,9 +32,9 @@
 import org.jabref.model.util.OptionalUtil;
 
 import com.google.common.util.concurrent.RateLimiter;
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONException;
-import kong.unirest.json.JSONObject;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONException;
+import kong.unirest.core.json.JSONObject;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/main/java/org/jabref/logic/importer/fetcher/GoogleScholar.java

@@ -27,7 +27,7 @@
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.paging.Page;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;

src/main/java/org/jabref/logic/importer/fetcher/GvkFetcher.java

@@ -20,7 +20,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 public class GvkFetcher extends AbstractIsbnFetcher implements SearchBasedParserFetcher {

src/main/java/org/jabref/logic/importer/fetcher/IEEE.java

@@ -31,9 +31,9 @@
 import org.jabref.model.entry.identifier.DOI;
 import org.jabref.model.entry.types.StandardEntryType;
 
-import kong.unirest.json.JSONArray;
-import kong.unirest.json.JSONObject;
-import org.apache.http.client.utils.URIBuilder;
+import kong.unirest.core.json.JSONArray;
+import kong.unirest.core.json.JSONObject;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/jabref/logic/importer/fetcher/INSPIREFetcher.java

@@ -28,7 +28,7 @@
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.field.UnknownField;
 
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 
 /**

src/main/java/org/jabref/logic/importer/fetcher/ISIDOREFetcher.java

@@ -28,7 +28,7 @@
 import org.jabref.model.entry.types.StandardEntryType;
 
 import jakarta.ws.rs.core.MediaType;
-import org.apache.http.client.utils.URIBuilder;
+import org.apache.hc.core5.net.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.jooq.lambda.Unchecked;
 import org.slf4j.Logger;