Merge remote-tracking branch 'origin/main' into 44-translationprovide…

…rs-sql
fxprunayre · Jun 3, 2024 · 25ef12f · 25ef12f
2 parents 71b4ebd + e98fa93
commit 25ef12f
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -33,9 +33,9 @@ jobs:
         if: ${{ github.event_name == 'pull_request' }}
         working-directory: docs/manual
         run: |
-          mike deploy --title "4.4 Latest" --alias-type=copy --update-aliases 4.4 latest
+          mike deploy --title "4.4" --alias-type=copy --update-aliases 4.4 latest
       - name: deploy latest docs to gh-pages branch
         if: ${{ github.event_name != 'pull_request' }}
         working-directory: docs/manual
         run: |
-          mike deploy --push --title "4.4 Latest" --alias-type=copy --update-aliases 4.4 latest
+          mike deploy --push --title "4.4" --alias-type=copy --update-aliases 4.4 latest
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -37,7 +37,7 @@ jobs:
     - name: Set up Maven
       uses: stCarolas/setup-maven@v5
       with:
-        maven-version: 3.6.3
+        maven-version: 3.8.3
     - name: Build with Maven
       run: |
         mvn -B -ntp -V install -DskipTests=true -Dmaven.javadoc.skip=true -Drelease -Pwith-doc
@@ -63,7 +63,7 @@ jobs:
     - name: Set up Maven
       uses: stCarolas/setup-maven@v5
       with:
-        maven-version: 3.6.3
+        maven-version: 3.8.3
     - name: Test with maven
       run: |
         mvn -B resources:resources@copy-index-schema-to-source -f web

diff --git a/.gitignore b/.gitignore
@@ -40,7 +40,12 @@ release/jetty/*
 schemas/*/doc/*/*.rst
 schematrons/.build
 target/
+
+# build and release
 transifex/transifex-format/
+build/
+web-ui/LICENSE
+web-ui/tx
 
 # web-app, clear using: mvn -f web/pom.xml clean:clean@reset
 

diff --git a/README.md b/README.md
@@ -4,9 +4,6 @@
 
 [![Build Status](https://github.com/geonetwork/core-geonetwork/actions/workflows/linux.yml/badge.svg?branch=main)](https://github.com/geonetwork/core-geonetwork/actions/workflows/linux.yml?query=branch%3Amain)
 
-## Open Source Security Foundation (OpenSSF) best practices status
-[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8626/badge)](https://www.bestpractices.dev/projects/8626)
-
 ## Features
 
 * Immediate search access to local and distributed geospatial catalogues
@@ -33,3 +30,6 @@ Developer documentation located in ``README.md`` files in the code-base:
 * General documentation for the project as a whole is in this [README.md](README.md)
 * [Software Development Documentation](/software_development/) provides instructions for setting up a development environment, building GeoNetwork, compiling user documentation, and making a releases.
 * Module specific documentation can be found in each module:
+
+## Open Source Security Foundation (OpenSSF) best practices status
+[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8626/badge)](https://www.bestpractices.dev/projects/8626)
diff --git a/cachingxslt/pom.xml b/cachingxslt/pom.xml
@@ -31,7 +31,7 @@
   <parent>
     <groupId>org.geonetwork-opensource</groupId>
     <artifactId>geonetwork</artifactId>
-    <version>4.4.3-SNAPSHOT</version>
+    <version>4.4.5-SNAPSHOT</version>
   </parent>
 
 

diff --git a/common/pom.xml b/common/pom.xml
@@ -31,7 +31,7 @@
   <parent>
     <groupId>org.geonetwork-opensource</groupId>
     <artifactId>geonetwork</artifactId>
-    <version>4.4.3-SNAPSHOT</version>
+    <version>4.4.5-SNAPSHOT</version>
   </parent>
 
 

diff --git a/common/src/main/java/org/fao/geonet/utils/Xml.java b/common/src/main/java/org/fao/geonet/utils/Xml.java
@@ -39,14 +39,7 @@
 import org.fao.geonet.utils.nio.NioPathAwareEntityResolver;
 import org.fao.geonet.utils.nio.NioPathHolder;
 import org.fao.geonet.utils.nio.PathStreamSource;
-import org.jdom.Attribute;
-import org.jdom.Content;
-import org.jdom.DocType;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.Text;
+import org.jdom.*;
 import org.jdom.filter.ElementFilter;
 import org.jdom.input.SAXBuilder;
 import org.jdom.output.Format;
@@ -64,27 +57,14 @@
 import javax.xml.XMLConstants;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.Unmarshaller;
-import javax.xml.transform.Result;
-import javax.xml.transform.Source;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.URIResolver;
+import javax.xml.transform.*;
 import javax.xml.transform.sax.SAXResult;
 import javax.xml.transform.stream.StreamResult;
 import javax.xml.transform.stream.StreamSource;
 import javax.xml.validation.Schema;
 import javax.xml.validation.SchemaFactory;
 import javax.xml.validation.ValidatorHandler;
-import java.io.BufferedOutputStream;
-import java.io.ByteArrayInputStream;
-import java.io.DataInputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.PrintStream;
-import java.io.StringReader;
+import java.io.*;
 import java.net.HttpURLConnection;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -99,14 +79,7 @@
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
+import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -403,22 +376,16 @@ public static Element transform(Element xml, Path styleSheetPath, Map<String, Ob
     /**
      * Transforms an xml tree putting the result to a stream (uses a stylesheet on disk).
      */
-    public static void transform(Element xml, Path styleSheetPath, OutputStream out) throws Exception {
+    public static void transform(Element xml, Path styleSheetPath, Map<String, Object> params, OutputStream out) throws Exception {
         StreamResult resStream = new StreamResult(out);
-        transform(xml, styleSheetPath, resStream, null);
+        transform(xml, styleSheetPath, resStream, params);
         out.flush();
     }
 
-
-    public static void transformXml(Element xml, Path styleSheetPath, OutputStream out) throws Exception {
-        StreamResult resStream = new StreamResult(out);
-        Map<String, Object> map = new HashMap<>();
-        map.put("geonet-force-xml", "xml");
-        transform(xml, styleSheetPath, resStream, map);
-        out.flush();
+    public static void transform(Element xml, Path styleSheetPath, OutputStream out) throws Exception {
+        transform(xml, styleSheetPath, new HashMap<>(), out);
     }
 
-    //--------------------------------------------------------------------------
 
     /**
      * Transforms an xml tree putting the result to a stream  - no parameters.
@@ -484,6 +451,9 @@ protected static Path resolvePath(Source s) throws URISyntaxException {
 
     /**
      * Transforms an xml tree putting the result to a stream with optional parameters.
+     * <p>
+     * Add a geonet-force-xml parameter to force the formatting to be xml.
+     * The preferred method is to define it using xsl:output.
      */
     public static void
     transform(Element xml, Path styleSheetPath, Result result, Map<String, Object> params) throws Exception {
@@ -515,13 +485,13 @@ protected static Path resolvePath(Source s) throws URISyntaxException {
                         t.setParameter(param.getKey(), param.getValue());
                     }
 
-                if (params.containsKey("geonet-force-xml")) {
-                    ((Controller) t).setOutputProperty("indent", "yes");
-                    ((Controller) t).setOutputProperty("method", "xml");
-                    ((Controller) t).setOutputProperty("{http://saxon.sf.net/}indent-spaces", "3");
+                    if (params.containsKey("geonet-force-xml")) {
+                        ((Controller) t).setOutputProperty("indent", "yes");
+                        ((Controller) t).setOutputProperty("method", "xml");
+                        ((Controller) t).setOutputProperty("{http://saxon.sf.net/}indent-spaces", "2");
+                    }
                 }
 
-                }
                 t.transform(srcXml, result);
             }
         }

diff --git a/core/pom.xml b/core/pom.xml
@@ -27,7 +27,7 @@
   <parent>
     <artifactId>geonetwork</artifactId>
     <groupId>org.geonetwork-opensource</groupId>
-    <version>4.4.3-SNAPSHOT</version>
+    <version>4.4.5-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

diff --git a/core/src/main/java/org/fao/geonet/kernel/SchemaManager.java b/core/src/main/java/org/fao/geonet/kernel/SchemaManager.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2001-2023 Food and Agriculture Organization of the
+ * Copyright (C) 2001-2024 Food and Agriculture Organization of the
  * United Nations (FAO-UN), United Nations World Food Programme (WFP)
  * and United Nations Environment Programme (UNEP)
  *
@@ -1383,7 +1383,6 @@ private void checkAppSupported(Element schemaPluginCatRoot) throws Exception {
                         " requires max Geonetwork version: " + majorAppVersionSupported + ", current is: " +
                         version + ". Skip load schema.");
                     removes.add(schemaInfo.getKey());
-                    continue;
                 }
             }
 
@@ -1901,7 +1900,7 @@ public boolean accept(Path entry) throws IOException {
         try (DirectoryStream<Path> schemaplugins = Files.newDirectoryStream(schemaPluginDir, xsdFilter)) {
             boolean missingXsdFiles = true;
             for (Path schemaplugin : schemaplugins) {
-                IO.copyDirectoryOrFile(schemaplugin, webAppDirSchemaXSD.resolve(schemaplugin), false);
+                IO.copyDirectoryOrFile(schemaplugin, webAppDirSchemaXSD.resolve(schemaplugin.getFileName()), false);
                 missingXsdFiles = false;
             }
 

diff --git a/core/src/main/java/org/fao/geonet/kernel/datamanager/IMetadataStatus.java b/core/src/main/java/org/fao/geonet/kernel/datamanager/IMetadataStatus.java
@@ -69,11 +69,14 @@ public interface IMetadataStatus {
     MetadataStatus setStatusExt(ServiceContext context, int id, int status, ISODate changeDate, String changeMessage) throws Exception;
 
     /**
-     * Set status of metadata id and do not reindex metadata id afterwards.
+     * Set status of metadata id and reindex metadata id afterwards based on updateIndex flag
+     *
+     * @param status metadata status to set
+     * @param updateIndex index update flag
      *
      * @return the saved status entity object
      */
-    MetadataStatus setStatusExt(MetadataStatus status) throws Exception;
+    MetadataStatus setStatusExt(MetadataStatus status, boolean updateIndex) throws Exception;
 
     /**
      * Set status of metadata id and reindex metadata id afterwards.

diff --git a/core/src/main/java/org/fao/geonet/kernel/datamanager/base/BaseMetadataStatus.java b/core/src/main/java/org/fao/geonet/kernel/datamanager/base/BaseMetadataStatus.java
@@ -160,9 +160,11 @@ public MetadataStatus setStatus(ServiceContext context, int id, int status, ISOD
     }
 
     @Override
-    public MetadataStatus setStatusExt(MetadataStatus metatatStatus) throws Exception {
+    public MetadataStatus setStatusExt(MetadataStatus metatatStatus, boolean updateIndex) throws Exception {
         metadataStatusRepository.save(metatatStatus);
-        metadataIndexer.indexMetadata(metatatStatus.getMetadataId() + "", true, IndexingMode.full);
+        if (updateIndex) {
+            metadataIndexer.indexMetadata(metatatStatus.getMetadataId() + "", true, IndexingMode.full);
+        }
         return metatatStatus;
     }
 

diff --git a/core/src/main/java/org/fao/geonet/kernel/datamanager/draft/DraftMetadataUtils.java b/core/src/main/java/org/fao/geonet/kernel/datamanager/draft/DraftMetadataUtils.java
@@ -589,7 +589,7 @@ protected String createDraft(ServiceContext context, String templateId, String g
 
                     List<MetadataStatus> listOfStatusChange = new ArrayList<>(1);
                     listOfStatusChange.add(metadataStatus);
-                    sa.onStatusChange(listOfStatusChange);
+                    sa.onStatusChange(listOfStatusChange, true);
                 }
             }
 

diff --git a/core/src/main/java/org/fao/geonet/kernel/metadata/DefaultStatusActions.java b/core/src/main/java/org/fao/geonet/kernel/metadata/DefaultStatusActions.java
@@ -136,7 +136,7 @@ public void onEdit(int id, boolean minorEdit) throws Exception {
      * @return
      * @throws Exception
      */
-    public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> listOfStatus) throws Exception {
+    public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> listOfStatus, boolean updateIndex) throws Exception {
 
         if (listOfStatus.stream().map(MetadataStatus::getMetadataId).distinct().count() != listOfStatus.size()) {
             throw new IllegalArgumentException("Multiple status update received on the same metadata");
@@ -179,16 +179,7 @@ public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> listOf
                 context.debug("Change status of metadata with id " + status.getMetadataId() + " from " + currentStatusId + " to " + statusId);
 
             // we know we are allowed to do the change, apply any side effects
-            boolean deleted = applyStatusChange(status.getMetadataId(), status, statusId);
-
-            // inform content reviewers if the status is submitted
-            try {
-                notify(getUserToNotify(status), status);
-            } catch (Exception e) {
-                context.warning(String.format(
-                    "Failed to send notification on status change for metadata %s with status %s. Error is: %s",
-                    status.getMetadataId(), status.getStatusValue().getId(), e.getMessage()));
-            }
+            boolean deleted = applyStatusChange(status.getMetadataId(), status, statusId, updateIndex);
 
             if (deleted) {
                 results.put(status.getMetadataId(), StatusChangeType.DELETED);
@@ -208,6 +199,15 @@ public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> listOf
                 }
             }
 
+            // inform content reviewers if the status is submitted
+            try {
+                notify(getUserToNotify(status), status);
+            } catch (Exception e) {
+                context.warning(String.format(
+                    "Failed to send notification on status change for metadata %s with status %s. Error is: %s",
+                    status.getMetadataId(), status.getStatusValue().getId(), e.getMessage()));
+            }
+
         }
 
         return results;
@@ -218,10 +218,10 @@ public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> listOf
      * eg. if APPROVED, publish a record,
      * if RETIRED, unpublish or delete the record.
      */
-    private boolean applyStatusChange(int metadataId, MetadataStatus status, String toStatusId) throws Exception {
+    private boolean applyStatusChange(int metadataId, MetadataStatus status, String toStatusId, boolean updateIndex) throws Exception {
         boolean deleted = false;
         if (!deleted) {
-            metadataStatusManager.setStatusExt(status);
+            metadataStatusManager.setStatusExt(status, updateIndex);
         }
         return deleted;
     }

diff --git a/core/src/main/java/org/fao/geonet/kernel/metadata/StatusActions.java b/core/src/main/java/org/fao/geonet/kernel/metadata/StatusActions.java
@@ -38,6 +38,6 @@ public interface StatusActions {
 
     public void onEdit(int id, boolean minorEdit) throws Exception;
 
-    public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> status) throws Exception;
+    public Map<Integer, StatusChangeType> onStatusChange(List<MetadataStatus> status, boolean updateIndex) throws Exception;
 
 }
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
@@ -552,6 +552,7 @@ private void checkIndexResponse(BulkResponse bulkItemResponses,
     static {
         arrayFields = ImmutableSet.<String>builder()
             .add(Geonet.IndexFieldNames.RECORDLINK)
+            .add("geom")
             .add("topic")
             .add("cat")
             .add("keyword")
@@ -664,14 +665,7 @@ public ObjectNode documentToJson(Element xml) {
                 || propertyName.endsWith("DateForResource")
                 || propertyName.startsWith("cl_");
 
-            if (name.equals("geom")) {
-                try {
-                    doc.set("geom", mapper.readTree(nodeElements.get(0).getTextNormalize()));
-                } catch (IOException e) {
-                    LOGGER.error("Parsing invalid geometry for JSON node {}. Error is: {}",
-                        nodeElements.get(0).getTextNormalize(), e.getMessage());
-                }
-            } else if (isArray) {
+            if (isArray) {
                 ArrayNode arrayNode = doc.putArray(propertyName);
                 for (Element node : nodeElements) {
                     if (isObject) {
@@ -817,8 +811,8 @@ public SearchResponse query(JsonNode jsonRequest, Set<String> includedFields,
         return client.query(defaultIndex, jsonRequest, null, includedFields, from, size);
     }
 
-    public Map<String, String> getFieldsValues(String id, Set<String> fields) throws IOException {
-        return client.getFieldsValues(defaultIndex, id, fields);
+    public Map<String, String> getFieldsValues(String id, Set<String> fields, String language) throws Exception {
+        return client.getFieldsValues(defaultIndex, id, fields, language);
     }
 
 

diff --git a/.../fao/geonet/kernel/security/openidconnect/bearer/GeonetworkJwtAuthenticationProvider.java b/.../fao/geonet/kernel/security/openidconnect/bearer/GeonetworkJwtAuthenticationProvider.java
@@ -52,7 +52,7 @@
 import org.springframework.security.oauth2.core.user.DefaultOAuth2User;
 import org.springframework.security.oauth2.core.user.OAuth2User;
 import org.springframework.security.oauth2.jwt.Jwt;
-import org.springframework.security.oauth2.server.resource.BearerTokenAuthenticationToken;
+import org.springframework.security.oauth2.server.resource.authentication.BearerTokenAuthenticationToken;
 import org.springframework.security.oauth2.server.resource.BearerTokenError;
 import org.springframework.security.oauth2.server.resource.BearerTokenErrorCodes;
 import org.springframework.security.oauth2.server.resource.authentication.JwtAuthenticationConverter;

diff --git a/core/src/main/java/org/fao/geonet/kernel/security/openidconnect/bearer/UserInfoCache.java b/core/src/main/java/org/fao/geonet/kernel/security/openidconnect/bearer/UserInfoCache.java
@@ -10,19 +10,13 @@
  */
 public class UserInfoCache {
 
-    static Object lockobj = new Object();
+    static final Object lockobj = new Object();
     Map<String, UserInfoCacheItem> cache = new HashMap<>();
 
     public UserInfoCacheItem getItem(String accessKey) {
         synchronized (lockobj) {
-            if (!cache.containsKey(accessKey))
-                return null;
-            UserInfoCacheItem item = cache.get(accessKey);
-            if (item.isExpired()) {
-                cache.remove(accessKey);
-                return null;
-            }
-            return item;
+            cache.entrySet().removeIf(e -> e.getValue().isExpired());
+            return cache.get(accessKey);
         }
     }