chore: Merge master

.github/workflows/run-api-tests.yml

@@ -8,7 +8,6 @@ on:
     branches:
       - master
   pull_request:
-    types: [ opened, labeled, synchronize ]
 concurrency:
   group: ${{ github.workflow}}-${{ github.ref }}
   cancel-in-progress: true
@@ -20,7 +19,6 @@ jobs:
       CORE_IMAGE_NAME: "dhis2/core-pr:${{ github.event_name == 'pull_request' && github.event.number || 'local' }}"
 
     runs-on: ubuntu-latest
-    if: "!contains(github.event.pull_request.labels.*.name, 'skip-api-tests')"
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK 17

dhis-2/dhis-api/pom.xml

@@ -97,6 +97,10 @@
       <groupId>org.hisp.dhis.rules</groupId>
       <artifactId>rule-engine</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.hisp.dhis</groupId>
+      <artifactId>json-tree</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.springframework.security</groupId>
       <artifactId>spring-security-core</artifactId>

dhis-2/dhis-api/src/main/java/org/hisp/dhis/dbms/DbmsManager.java

@@ -27,7 +27,6 @@
  */
 package org.hisp.dhis.dbms;
 
-import java.io.Serializable;
 import java.util.List;
 
 /**
@@ -47,10 +46,4 @@ public interface DbmsManager {
   boolean tableExists(String tableName);
 
   List<List<Object>> getTableContent(String table);
-
-  void evictObject(Object object);
-
-  boolean contains(Object object);
-
-  Serializable getIdentifier(Object object);
 }

dhis-2/dhis-api/src/main/java/org/hisp/dhis/reservedvalue/ReservedValueStore.java

@@ -42,8 +42,6 @@ public interface ReservedValueStore extends GenericStore<ReservedValue> {
   List<ReservedValue> getAvailableValues(
       ReservedValue reservedValue, List<String> values, String ownerObject);
 
-  List<ReservedValue> reserveValuesJpa(ReservedValue reservedValue, List<String> values);
-
   int getNumberOfUsedValues(ReservedValue reservedValue);
 
   boolean useReservedValue(String ownerUID, String value);

dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobConfigurationService.java

@@ -30,7 +30,9 @@
 import java.io.InputStream;
 import java.util.List;
 import java.util.Map;
+import javax.annotation.Nonnull;
 import org.hisp.dhis.feedback.ConflictException;
+import org.hisp.dhis.jsontree.JsonObject;
 import org.hisp.dhis.schema.Property;
 import org.springframework.util.MimeType;
 
@@ -160,6 +162,13 @@ String create(JobConfiguration config, MimeType contentType, InputStream content
    */
   List<JobConfiguration> getStaleConfigurations(int staleForSeconds);
 
+  /**
+   * @param params query parameters (criteria) to find
+   * @return all job configurations that match the query parameters
+   */
+  @Nonnull
+  List<JsonObject> findJobRunErrors(@Nonnull JobRunErrorsParams params);
+
   /**
    * Get a map of parameter classes with appropriate properties This can be used for a frontend app
    * or for other appropriate applications which needs information about the jobs in the system.

dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobConfigurationStore.java

@@ -115,6 +115,13 @@ public interface JobConfigurationStore extends GenericDimensionalObjectStore<Job
    */
   Stream<JobConfiguration> getDueJobConfigurations(boolean includeWaiting);
 
+  /**
+   * @param params query parameters (criteria) to find
+   * @return all job configurations that match the query parameters
+   */
+  @Nonnull
+  Stream<String> findJobRunErrors(@Nonnull JobRunErrorsParams params);
+
   /**
    * @return A list of all job types that are currently in {@link JobStatus#RUNNING} state.
    */

dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobProgress.java

@@ -142,12 +142,18 @@ default boolean isSkipCurrentStage() {
   Error reporting API:
   */
 
-  default void addError(ErrorCode code, String uid, String type, Integer index, String... args) {
-    addError(code, uid, type, index, List.of(args));
+  default void addError(
+      @Nonnull ErrorCode code, @CheckForNull String uid, @Nonnull String type, String... args) {
+    addError(code, uid, type, List.of(args));
   }
 
-  default void addError(ErrorCode code, String uid, String type, Integer index, List<String> args) {
-    // default implementation is a NOOP, we don't remember or handle the error
+  default void addError(
+      @Nonnull ErrorCode code,
+      @CheckForNull String uid,
+      @Nonnull String type,
+      @Nonnull List<String> args) {
+    // is overridden by a tracker that collects errors
+    // default is to not collect errors
   }
 
   /*
@@ -590,10 +596,13 @@ public Progress(
     }
 
     public void addError(Error error) {
-      errors
-          .computeIfAbsent(error.getId(), key -> new ConcurrentHashMap<>())
-          .computeIfAbsent(error.getCode(), key2 -> new ConcurrentLinkedQueue<>())
-          .add(error);
+      Queue<Error> sameObjectAndCode =
+          errors
+              .computeIfAbsent(error.getId(), key -> new ConcurrentHashMap<>())
+              .computeIfAbsent(error.getCode(), key2 -> new ConcurrentLinkedQueue<>());
+      if (sameObjectAndCode.stream().noneMatch(e -> e.args.equals(error.args))) {
+        sameObjectAndCode.add(error);
+      }
     }
 
     public boolean hasErrors() {
@@ -619,13 +628,6 @@ final class Error {
     /** The type of the object identified by #id that has the error */
     @Nonnull @JsonProperty private final String type;
 
-    /**
-     * The row index in the payload of the import. This is the index in the list of objects of a
-     * single type. This means the same index occurs for each object type. For some imports this
-     * information is not available.
-     */
-    @CheckForNull @JsonProperty private final Integer index;
-
     /** The arguments used in the {@link #code}'s {@link ErrorCode#getMessage()} template */
     @Nonnull @JsonProperty private final List<String> args;
 
@@ -642,12 +644,10 @@ public Error(
         @Nonnull @JsonProperty("code") ErrorCode code,
         @Nonnull @JsonProperty("id") String id,
         @Nonnull @JsonProperty("type") String type,
-        @CheckForNull @JsonProperty("index") Integer index,
         @Nonnull @JsonProperty("args") List<String> args) {
       this.code = code;
       this.id = id;
       this.type = type;
-      this.index = index;
       this.args = args;
     }
   }

dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobRunErrorsParams.java

@@ -0,0 +1,75 @@
+/*
+ * Copyright (c) 2004-2023, University of Oslo
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ * Neither the name of the HISP project nor the names of its contributors may
+ * be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.hisp.dhis.scheduling;
+
+import java.util.Date;
+import java.util.List;
+import javax.annotation.CheckForNull;
+import lombok.Data;
+import lombok.experimental.Accessors;
+import org.hisp.dhis.common.OpenApi;
+import org.hisp.dhis.common.UID;
+import org.hisp.dhis.feedback.ErrorCode;
+import org.hisp.dhis.user.User;
+
+/**
+ * Query params when searching for {@link JobConfiguration}s with errors.
+ *
+ * <p>A match has to satisfy all filters (AND logic) but only one of the given codes or object
+ * {@link UID} (OR logic).
+ *
+ * <p>If any of the criteria is not defined it has no filter effect.
+ *
+ * @author Jan Bernitt
+ */
+@Data
+@Accessors(chain = true)
+public class JobRunErrorsParams {
+
+  @OpenApi.Ignore @CheckForNull private UID job;
+
+  /** The user that ran the job */
+  @OpenApi.Property({UID.class, User.class})
+  @CheckForNull
+  private UID user;
+
+  /** The earliest date the job ran that should be included */
+  @CheckForNull private Date from;
+
+  /** The latest date the job ran that should be included */
+  @CheckForNull private Date to;
+
+  /** The codes to select, any match combined */
+  @CheckForNull private List<ErrorCode> code;
+
+  /** The object with errors to select, any match combined */
+  @CheckForNull private List<UID> object;
+
+  /** The {@link JobType} with errors to select, any match combined */
+  @CheckForNull private List<JobType> type;
+}

dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/CurrentUserService.java

@@ -73,6 +73,7 @@ public String getCurrentUsername() {
     return CurrentUserUtil.getCurrentUsername();
   }
 
+  @Transactional(readOnly = true)
   public User getCurrentUser() {
     String username = CurrentUserUtil.getCurrentUsername();
 

dhis-2/dhis-services/dhis-service-administration/pom.xml

@@ -101,8 +101,8 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>org.hibernate</groupId>
-      <artifactId>hibernate-core</artifactId>
+      <groupId>javax.persistence</groupId>
+      <artifactId>javax.persistence-api</artifactId>
     </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>

dhis-2/dhis-services/dhis-service-administration/src/main/java/org/hisp/dhis/dataintegrity/hibernate/HibernateDataIntegrityStore.java

@@ -31,8 +31,9 @@
 
 import java.util.Date;
 import java.util.List;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
 import lombok.RequiredArgsConstructor;
-import org.hibernate.SessionFactory;
 import org.hisp.dhis.dataintegrity.DataIntegrityCheck;
 import org.hisp.dhis.dataintegrity.DataIntegrityDetails;
 import org.hisp.dhis.dataintegrity.DataIntegrityDetails.DataIntegrityIssue;
@@ -50,13 +51,13 @@
 @Repository
 @RequiredArgsConstructor
 public class HibernateDataIntegrityStore implements DataIntegrityStore {
-  private final SessionFactory sessionFactory;
+  @PersistenceContext private final EntityManager entityManager;
 
   @Override
   @Transactional(readOnly = true)
   public DataIntegritySummary querySummary(DataIntegrityCheck check, String sql) {
     Date startTime = new Date();
-    Object summary = sessionFactory.getCurrentSession().createNativeQuery(sql).getSingleResult();
+    Object summary = entityManager.createNativeQuery(sql).getSingleResult();
     return new DataIntegritySummary(
         check, startTime, new Date(), null, parseCount(summary), parsePercentage(summary));
   }
@@ -66,7 +67,7 @@ public DataIntegritySummary querySummary(DataIntegrityCheck check, String sql) {
   public DataIntegrityDetails queryDetails(DataIntegrityCheck check, String sql) {
     Date startTime = new Date();
     @SuppressWarnings("unchecked")
-    List<Object[]> rows = sessionFactory.getCurrentSession().createNativeQuery(sql).getResultList();
+    List<Object[]> rows = entityManager.createNativeQuery(sql).getResultList();
     return new DataIntegrityDetails(
         check,
         startTime,

dhis-2/dhis-services/dhis-service-administration/src/main/java/org/hisp/dhis/merge/orgunit/handler/DataOrgUnitMergeHandler.java

@@ -29,8 +29,8 @@
 
 import static org.hisp.dhis.common.IdentifiableObjectUtils.getIdentifiers;
 
+import javax.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
-import org.hibernate.SessionFactory;
 import org.hisp.dhis.common.IdentifiableObjectUtils;
 import org.hisp.dhis.dataapproval.DataApprovalAuditService;
 import org.hisp.dhis.dataset.DataSetService;
@@ -55,7 +55,7 @@
 @Transactional
 @RequiredArgsConstructor
 public class DataOrgUnitMergeHandler {
-  private final SessionFactory sessionFactory;
+  private final EntityManager entityManager;
 
   private final NamedParameterJdbcTemplate jdbcTemplate;
 
@@ -201,11 +201,10 @@ public void mergeInterpretations(OrgUnitMergeRequest request) {
   }
 
   private void migrate(String hql, OrgUnitMergeRequest request) {
-    sessionFactory
-        .getCurrentSession()
+    entityManager
         .createQuery(hql)
         .setParameter("target", request.getTarget())
-        .setParameterList("sources", IdentifiableObjectUtils.getIdentifiers(request.getSources()))
+        .setParameter("sources", IdentifiableObjectUtils.getIdentifiers(request.getSources()))
         .executeUpdate();
   }
 }

dhis-2/dhis-services/dhis-service-administration/src/main/java/org/hisp/dhis/merge/orgunit/handler/TrackerOrgUnitMergeHandler.java

@@ -27,8 +27,8 @@
  */
 package org.hisp.dhis.merge.orgunit.handler;
 
+import javax.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
-import org.hibernate.SessionFactory;
 import org.hisp.dhis.common.IdentifiableObjectUtils;
 import org.hisp.dhis.merge.orgunit.OrgUnitMergeRequest;
 import org.springframework.stereotype.Service;
@@ -42,7 +42,7 @@
 @Service
 @RequiredArgsConstructor
 public class TrackerOrgUnitMergeHandler {
-  private final SessionFactory sessionFactory;
+  private final EntityManager entityManager;
 
   @Transactional
   public void mergeProgramMessages(OrgUnitMergeRequest request) {
@@ -90,11 +90,10 @@ public void mergeTrackedEntities(OrgUnitMergeRequest request) {
   }
 
   private void migrate(String hql, OrgUnitMergeRequest request) {
-    sessionFactory
-        .getCurrentSession()
+    entityManager
         .createQuery(hql)
         .setParameter("target", request.getTarget())
-        .setParameterList("sources", IdentifiableObjectUtils.getIdentifiers(request.getSources()))
+        .setParameter("sources", IdentifiableObjectUtils.getIdentifiers(request.getSources()))
         .executeUpdate();
   }
 }

dhis-2/dhis-services/dhis-service-administration/src/main/java/org/hisp/dhis/split/orgunit/handler/DataOrgUnitSplitHandler.java

@@ -27,9 +27,9 @@
  */
 package org.hisp.dhis.split.orgunit.handler;
 
+import javax.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
-import org.hibernate.SessionFactory;
 import org.hisp.dhis.split.orgunit.OrgUnitSplitRequest;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
@@ -46,7 +46,7 @@ public class DataOrgUnitSplitHandler {
 
   private static final String PARAM_SOURCE = "source";
 
-  private final SessionFactory sessionFactory;
+  private final EntityManager entityManager;
 
   @Transactional
   public void splitData(OrgUnitSplitRequest request) {
@@ -74,8 +74,7 @@ private void migrate(OrgUnitSplitRequest request, String entity, String property
 
     log.debug("Update data HQL: '{}'", hql);
 
-    sessionFactory
-        .getCurrentSession()
+    entityManager
         .createQuery(hql)
         .setParameter("source", request.getSource())
         .setParameter("target", request.getPrimaryTarget())