Merge tag '4.2.6' into 4.2.x-rebase

georchestra · Nov 15, 2023 · a626eba · a626eba
2 parents 56f1e0c + d7b4ae6
commit a626eba
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diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -0,0 +1,67 @@
+name: Linux GitHub CI
+
+on: [pull_request,push,workflow_dispatch]
+
+env:
+  MAVEN_OPTS: -Dmaven.wagon.httpconnectionManager.ttlSeconds=25 -Dmaven.wagon.http.retryHandler.count=3 -Xmx512m -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS
+  TAKARI_SMART_BUILDER_VERSION: 0.6.1
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-22.04
+            jdk: 8
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        # 500 commits, set to 0 to get all
+        fetch-depth: 500
+        submodules: 'recursive'
+        show-progress: 'false'
+    - name: Set up JDK
+      uses: actions/[email protected]
+      with:
+        distribution: 'temurin'
+        java-version: ${{ matrix.jdk }}
+        cache: 'maven'
+    - name: Build with Maven
+      run: mvn -B -V install -DskipTests=true -Dmaven.javadoc.skip=true
+    - name: Remove SNAPSHOT jars from repository
+      run: |
+        find ~/.m2/repository -name "*SNAPSHOT*" -type d | xargs rm -rf {}
+    - name: Remove Schema 3.8 jars from repository
+      run: |
+        find ~/.m2/repository -name "*3.8*" -type d | xargs rm -rf {}
+
+  QA:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        # 500 commits, set to 0 to get all
+        fetch-depth: 500
+        submodules: 'recursive'
+        show-progress: 'false'
+    - name: Set up JDK
+      uses: actions/[email protected]
+      with:
+        distribution: 'temurin'
+        java-version: 8
+        cache: 'maven'
+    - name: Set up Maven
+      uses: stCarolas/setup-maven@v4
+      with:
+        maven-version: 3.6.3
+    - name: Test with maven
+      run: |
+        mvn resources:resources@copy-index-schema-to-source -f web
+        mvn -B -V -fae verify -Pit
+    - name: Remove SNAPSHOT jars from repository
+      run: |
+        find ~/.m2/repository -name "*SNAPSHOT*" -type d | xargs rm -rf {}
+    - name: Remove Schema 3.8 jars from repository
+      run: |
+        find ~/.m2/repository -name "*3.8*" -type d | xargs rm -rf {}
diff --git a/core/pom.xml b/core/pom.xml
@@ -128,18 +128,6 @@
       <artifactId>log4j-core</artifactId>
       <version>${log4j2.version}</version>
     </dependency>
-    <!-- bridge java util logging api based on logging.properties -->
-    <dependency>
-      <groupId>org.apache.logging.log4j</groupId>
-      <artifactId>log4j-jul</artifactId>
-      <version>${log4j2.version}</version>
-    </dependency>
-    <!-- bridge slf4j api for testig wtih apacheds -->
-    <dependency>
-      <groupId>org.apache.logging.log4j</groupId>
-      <artifactId>log4j-slf4j-impl</artifactId>
-      <scope>test</scope>
-    </dependency>
     <!-- log4j 2 logging configured via log4j2.xml -->
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
@@ -454,19 +442,10 @@
       <groupId>com.github.librepdf</groupId>
       <artifactId>openpdf</artifactId>
     </dependency>
-    <dependency>
-      <groupId>com.github.librepdf</groupId>
-      <artifactId>openpdf</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.mapfish.print</groupId>
       <artifactId>print-lib</artifactId>
       <exclusions>
-        <exclusion>
-          <!-- provided by openpdf -->
-          <groupId>com.itextpdf</groupId>
-          <artifactId>itextpdf</artifactId>
-        </exclusion>
         <exclusion>
           <!-- provided by openpdf -->
           <groupId>com.itextpdf</groupId>

diff --git a/core/src/main/java/jeeves/config/springutil/JeevesNodeAwareLogoutSuccessHandler.java b/core/src/main/java/jeeves/config/springutil/JeevesNodeAwareLogoutSuccessHandler.java
@@ -88,14 +88,14 @@ protected String determineTargetUrl(HttpServletRequest request, HttpServletRespo
 
                     String siteHost = settingManager.getValue(Settings.SYSTEM_SERVER_HOST);
                     String siteProtocol = settingManager.getValue(Settings.SYSTEM_SERVER_PROTOCOL);
-
+                    
                     // some conditional logic to handle the case where there's no port in the settings
                     SettingInfo si = new SettingInfo();
-                    int sitePort = si.getSitePort();
+                    int sitePort = si.getSitePort(); 
 
                     if (!hostName.equalsIgnoreCase(siteHost) ||
-                            !protocol.equalsIgnoreCase(siteProtocol) ||
-                            port != sitePort) {
+                        !protocol.equalsIgnoreCase(siteProtocol) ||
+                        port != sitePort) {
                         urlPatternValue = getDefaultTargetUrl();
                     }
                 } catch (MalformedURLException e) {

diff --git a/core/src/main/java/org/fao/geonet/kernel/AccessManager.java b/core/src/main/java/org/fao/geonet/kernel/AccessManager.java
@@ -23,7 +23,6 @@
 
 package org.fao.geonet.kernel;
 
-import static org.fao.geonet.kernel.setting.Settings.SYSTEM_METADATAPRIVS_PUBLICATIONBYGROUPOWNERONLY;
 import jeeves.server.UserSession;
 import jeeves.server.context.ServiceContext;
 import org.apache.commons.lang.StringUtils;

diff --git a/core/src/main/java/org/fao/geonet/kernel/GeonetworkDataDirectory.java b/core/src/main/java/org/fao/geonet/kernel/GeonetworkDataDirectory.java
@@ -210,6 +210,17 @@ public static File getLogfile() {
         return Log.getLogfile();
     }
 
+    /**
+     * Logfile location as determined from appender, or system property, or default.
+     * <p>
+     * Note this code is duplicated with the deprecated {@code LogConfig}.
+     *
+     * @return logfile location, or {@code null} if unable to determine
+     */
+    public static File getLogfile() {
+        return Log.getLogfile();
+    }
+
     /**
      * Determines the location of a property based on the
      * following lookup mechanism:

diff --git a/core/src/main/java/org/fao/geonet/kernel/Thesaurus.java b/core/src/main/java/org/fao/geonet/kernel/Thesaurus.java
@@ -125,9 +125,6 @@ public class Thesaurus {
     private Cache<String, Object> THESAURUS_SEARCH_CACHE;
 
 
-    private Cache<String, Object> THESAURUS_SEARCH_CACHE;
-
-
     /**
      * Available for subclasses.
      */

diff --git a/core/src/main/java/org/fao/geonet/kernel/datamanager/base/BaseMetadataManager.java b/core/src/main/java/org/fao/geonet/kernel/datamanager/base/BaseMetadataManager.java
@@ -49,7 +49,6 @@
 import org.fao.geonet.kernel.schema.SchemaPlugin;
 import org.fao.geonet.kernel.search.EsSearchManager;
 import org.fao.geonet.kernel.search.IndexingMode;
-import org.fao.geonet.kernel.search.IndexingMode;
 import org.fao.geonet.kernel.search.index.BatchOpsMetadataReindexer;
 import org.fao.geonet.kernel.setting.SettingManager;
 import org.fao.geonet.kernel.setting.Settings;
@@ -742,7 +741,8 @@ public synchronized AbstractMetadata updateMetadata(final ServiceContext context
             session.removeProperty(Geonet.Session.VALIDATION_REPORT + metadataId);
         }
         String schema = metadataSchemaUtils.getMetadataSchema(metadataId);
-final AbstractMetadata metadata = metadataUtils.findOne(metadataId);
+
+        final AbstractMetadata metadata = metadataUtils.findOne(metadataId);
 
         if (updateDateStamp) {
             if (StringUtils.isEmpty(changeDate)) {
@@ -752,6 +752,7 @@ public synchronized AbstractMetadata updateMetadata(final ServiceContext context
                 metadata.getDataInfo().setChangeDate(new ISODate(changeDate));
             }
         }
+
         String uuidBeforeUfo = null;
         if (ufo) {
             String parentUuid = null;

diff --git a/core/src/main/java/org/fao/geonet/kernel/search/EsSearchManager.java b/core/src/main/java/org/fao/geonet/kernel/search/EsSearchManager.java
@@ -212,7 +212,7 @@ private void addMDFields(Element doc, Path schemaDir,
                              IndexingMode indexingMode) {
         final Path styleSheet = getXSLTForIndexing(schemaDir, metadataType);
         try {
-            Map<String, Object> indexParams = new HashMap<String, Object>();
+            Map<String, Object> indexParams = new HashMap<>();
             indexParams.put("fastIndexMode", indexingMode.equals(IndexingMode.core));
 
             Element fields = Xml.transform(metadata, styleSheet, indexParams);

diff --git a/core/src/main/java/org/fao/geonet/kernel/security/openidconnect/OidcUser2GeonetworkUser.java b/core/src/main/java/org/fao/geonet/kernel/security/openidconnect/OidcUser2GeonetworkUser.java
@@ -161,9 +161,6 @@ public UserDetails getUserDetails(OidcIdToken idToken, Map attributes, boolean w
      */
     //from keycloak
     protected void updateGroups(Map<Profile, List<String>> profileGroups, User user) {
-        // First we remove all previous groups
-        userGroupRepository.deleteAll(UserGroupSpecs.hasUserId(user.getId()));
-
         Set<UserGroup> userGroups = new HashSet<>();
 
         // Now we add the groups

diff --git a/core/src/test/java/org/fao/geonet/kernel/LocalXLinksInMetadataIntegrationTest.java b/core/src/test/java/org/fao/geonet/kernel/LocalXLinksInMetadataIntegrationTest.java
@@ -110,8 +110,6 @@ public void testResolveLocalXLink() throws Exception {
         String id = _dataManager.insertMetadata(context, schema, metadata, uuid, owner, groupOwner, source, metadataType, null,
             null, createDate, changeDate, false, IndexingMode.none);
 
-        SpringLocalServiceInvoker mockInvoker = resetAndGetMockInvoker();
-
         String keyword1 = "World";
         Element element1 = new SAXBuilder().build(new StringReader(String.format(responseTemplate, keyword1))).getRootElement();
         when(springLocalServiceInvoker.invoke(any(String.class))).thenReturn(element1);

diff --git a/csw-server/src/main/java/org/fao/geonet/component/csw/Transaction.java b/csw-server/src/main/java/org/fao/geonet/component/csw/Transaction.java
@@ -23,8 +23,6 @@
 
 package org.fao.geonet.component.csw;
 
-import org.fao.geonet.kernel.search.IndexingMode;
-import org.locationtech.jts.util.Assert;
 import jeeves.server.UserSession;
 import jeeves.server.context.ServiceContext;
 import org.fao.geonet.ApplicationContextHolder;
@@ -360,6 +358,7 @@ private int updateTransaction(Element request, Element xml, ServiceContext conte
             }
 
             beforeMetadata = metadataUtils.findOneByUuid(uuid).getXmlData(false);
+
             String language = context.getLanguage();
             dataMan.updateMetadata(context, id, xml,
                 applyValidation, applyUpdateFixedInfo,

diff --git a/docs/manual/overrides/.icons/.DS_Store b/docs/manual/overrides/.icons/.DS_Store
diff --git a/docs/manual/pom.xml b/docs/manual/pom.xml
@@ -27,7 +27,7 @@
   <parent>
     <artifactId>gn-docs</artifactId>
     <groupId>org.geonetwork-opensource</groupId>
-    <version>4.2.6-0</version>
+    <version>4.2.6-georchestra</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>gn-guide</artifactId>

diff --git a/doi/src/main/java/org/fao/geonet/doi/client/DoiClient.java b/doi/src/main/java/org/fao/geonet/doi/client/DoiClient.java
diff --git a/doi/src/main/java/org/fao/geonet/doi/client/DoiManager.java b/doi/src/main/java/org/fao/geonet/doi/client/DoiManager.java
@@ -301,11 +301,6 @@ private void checkPreConditions(AbstractMetadata metadata, String doi) throws Do
                 .withDescriptionKey("exception.doi.missingSavedquery.description",
                     new String[]{ metadata.getUuid(), schema.getName(),
                     SavedQuery.DOI_GET, e.getMessage(),
-                    schema.getName() })
-                .withMessageKey("exception.doi.missingSavedquery")
-                .withDescriptionKey("exception.doi.missingSavedquery.description",
-                    new String[]{ metadata.getUuid(), schema.getName(),
-                    DOI_GET_SAVED_QUERY, e.getMessage(),
                     schema.getName() });
         }
     }

diff --git a/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/AbstractHarvester.java b/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/AbstractHarvester.java
@@ -26,7 +26,6 @@
 import jeeves.server.UserSession;
 import jeeves.server.context.ServiceContext;
 import org.apache.commons.lang.StringUtils;
-import org.apache.logging.log4j.ThreadContext;
 import org.fao.geonet.Logger;
 import org.fao.geonet.constants.Geonet;
 import org.fao.geonet.csw.common.exceptions.InvalidParameterValueEx;
@@ -606,6 +605,7 @@ protected OperResult harvest() {
                 cancelMonitor.set(false);
                 try {
                     String logfile = LogUtil.initializeHarvesterLog(getType(), this.getParams().getName());
+
                     this.log.info("Starting harvesting of " + this.getParams().getName());
                     error = null;
                     errors.clear();

diff --git a/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/geonet/Aligner.java b/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/geonet/Aligner.java
@@ -43,7 +43,6 @@
 import org.fao.geonet.kernel.harvest.harvester.*;
 import org.fao.geonet.kernel.mef.*;
 import org.fao.geonet.kernel.search.IndexingMode;
-import org.fao.geonet.kernel.search.IndexingMode;
 import org.fao.geonet.kernel.setting.SettingManager;
 import org.fao.geonet.kernel.setting.Settings;
 import org.fao.geonet.repository.GroupRepository;

diff --git a/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleUrl/Aligner.java b/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleUrl/Aligner.java
diff --git a/integration-test/pom.xml b/integration-test/pom.xml
@@ -60,7 +60,7 @@
 
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
-      <artifactId>log4j-slf4j18-impl</artifactId>
+      <artifactId>log4j-slf4j-impl</artifactId>
       <version>${log4j2.version}</version>
     </dependency>