Merge branch 'batchhandler-autoclose' of github.com:dhis2/dhis2-core …

…into batchhandler-autoclose

dhis-2/dhis-api/src/main/java/org/hisp/dhis/fileresource/FileResourceService.java

@@ -32,18 +32,33 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.net.URI;
+import java.time.Duration;
 import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.Optional;
 import javax.annotation.CheckForNull;
 import javax.annotation.Nonnull;
+import org.hisp.dhis.feedback.ConflictException;
+import org.hisp.dhis.feedback.NotFoundException;
 
 /**
  * @author Halvdan Hoem Grelland
  */
 public interface FileResourceService {
+
+  @CheckForNull
   FileResource getFileResource(String uid);
 
+  /**
+   * Get the {@link FileResource} with the given ID
+   *
+   * @param uid the resource to fetch
+   * @return the file resource
+   * @throws NotFoundException when no such file resource exits
+   */
+  @Nonnull
+  FileResource getExistingFileResource(String uid) throws NotFoundException;
+
   /**
    * Lookup a {@link FileResource} by uid and {@link FileResourceDomain}.
    *
@@ -83,7 +98,12 @@ public interface FileResourceService {
 
   void deleteFileResource(FileResource fileResource);
 
-  InputStream getFileResourceContent(FileResource fileResource);
+  @Nonnull
+  InputStream getFileResourceContent(FileResource fileResource) throws ConflictException;
+
+  @Nonnull
+  InputStream getFileResourceContent(FileResource fileResource, Duration timeout)
+      throws ConflictException;
 
   /** Copy fileResource content to outputStream and Return File content length */
   void copyFileResourceContent(FileResource fileResource, OutputStream outputStream)

dhis-2/dhis-api/src/main/java/org/hisp/dhis/fileresource/FileResourceStorageStatus.java

@@ -33,6 +33,5 @@
 public enum FileResourceStorageStatus {
   NONE, // No content stored
   PENDING, // In transit to store, not available
-  FAILED, // Storing the resource failed
   STORED // Is available from store
 }

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

@@ -206,6 +206,7 @@ public boolean isUsingNotifications() {
         || this == DATAVALUE_IMPORT
         || this == COMPLETE_DATA_SET_REGISTRATION_IMPORT
         || this == METADATA_IMPORT
+        || this == TRACKER_IMPORT_JOB
         || this == GEOJSON_IMPORT;
   }
 
@@ -231,7 +232,7 @@ public boolean isUsingErrorNotification() {
    *     the ready jobs per type is attempted to start in a single loop cycle
    */
   public boolean isUsingContinuousExecution() {
-    return this == METADATA_IMPORT;
+    return this == METADATA_IMPORT || this == TRACKER_IMPORT_JOB;
   }
 
   public boolean hasJobParameters() {

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/fileresource/DefaultFileResourceService.java

@@ -27,6 +27,10 @@
  */
 package org.hisp.dhis.fileresource;
 
+import static java.lang.System.currentTimeMillis;
+import static java.time.Duration.ofMillis;
+import static java.time.Duration.ofSeconds;
+
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
@@ -43,7 +47,9 @@
 import lombok.RequiredArgsConstructor;
 import org.hibernate.SessionFactory;
 import org.hisp.dhis.common.IllegalQueryException;
+import org.hisp.dhis.feedback.ConflictException;
 import org.hisp.dhis.feedback.ErrorCode;
+import org.hisp.dhis.feedback.NotFoundException;
 import org.hisp.dhis.fileresource.events.BinaryFileSavedEvent;
 import org.hisp.dhis.fileresource.events.FileDeletedEvent;
 import org.hisp.dhis.fileresource.events.FileSavedEvent;
@@ -86,6 +92,15 @@ public class DefaultFileResourceService implements FileResourceService {
   // FileResourceService implementation
   // -------------------------------------------------------------------------
 
+  @Nonnull
+  @Override
+  @Transactional(readOnly = true)
+  public FileResource getExistingFileResource(String uid) throws NotFoundException {
+    FileResource fr = fileResourceStore.getByUid(uid);
+    if (fr == null) throw new NotFoundException(FileResource.class, uid);
+    return fr;
+  }
+
   @Override
   @Transactional(readOnly = true)
   public FileResource getFileResource(String uid) {
@@ -228,26 +243,43 @@ public void deleteFileResource(FileResource fileResource) {
   }
 
   @Override
-  @Transactional(readOnly = true)
-  public InputStream getFileResourceContent(FileResource fileResource) {
-    return fileResourceContentStore.getFileResourceContent(fileResource.getStorageKey());
+  @Nonnull
+  public InputStream getFileResourceContent(FileResource fileResource) throws ConflictException {
+    return getFileResourceContent(fileResource, ofSeconds(10));
+  }
+
+  @Nonnull
+  @Override
+  public InputStream getFileResourceContent(FileResource fileResource, java.time.Duration timeout)
+      throws ConflictException {
+    String key = fileResource.getStorageKey();
+    InputStream content = fileResourceContentStore.getFileResourceContent(key);
+    long since = currentTimeMillis();
+    while (content == null && !timeout.minus(ofMillis(currentTimeMillis() - since)).isNegative()) {
+      try {
+        Thread.sleep(50);
+      } catch (InterruptedException e) {
+        Thread.currentThread().interrupt();
+      }
+      content = fileResourceContentStore.getFileResourceContent(key);
+    }
+    if (content == null)
+      throw new ConflictException("File resource exists but content input stream was null");
+    return content;
   }
 
   @Override
-  @Transactional(readOnly = true)
   public long getFileResourceContentLength(FileResource fileResource) {
     return fileResourceContentStore.getFileResourceContentLength(fileResource.getStorageKey());
   }
 
   @Override
-  @Transactional(readOnly = true)
   public void copyFileResourceContent(FileResource fileResource, OutputStream outputStream)
       throws IOException, NoSuchElementException {
     fileResourceContentStore.copyContent(fileResource.getStorageKey(), outputStream);
   }
 
   @Override
-  @Transactional(readOnly = true)
   public byte[] copyFileResourceContent(FileResource fileResource)
       throws IOException, NoSuchElementException {
     return fileResourceContentStore.copyContent(fileResource.getStorageKey());

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/fileresource/JCloudsFileResourceContentStore.java

@@ -194,6 +194,7 @@ public InputStream getFileResourceContent(String key) {
     final Blob blob = getBlob(key);
 
     if (blob == null) {
+
       return null;
     }
 

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/scheduling/HibernateJobConfigurationStore.java

@@ -29,6 +29,7 @@
 
 import static java.lang.Math.max;
 import static java.util.stream.Collectors.toSet;
+import static org.springframework.transaction.annotation.Propagation.REQUIRES_NEW;
 
 import java.util.List;
 import java.util.Set;
@@ -45,6 +46,7 @@
 import org.springframework.context.ApplicationEventPublisher;
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.stereotype.Repository;
+import org.springframework.transaction.annotation.Transactional;
 
 /**
  * @author Jan Bernitt
@@ -242,6 +244,7 @@ public Stream<JobConfiguration> getDueJobConfigurations(boolean includeWaiting)
   }
 
   @Override
+  @Transactional(propagation = REQUIRES_NEW)
   public boolean tryExecuteNow(@Nonnull String jobId) {
     // language=SQL
     String sql =

dhis-2/dhis-services/dhis-service-dxf2/src/main/java/org/hisp/dhis/dxf2/datavalueset/DataValueSetImportValidator.java

@@ -54,7 +54,6 @@
 import org.hisp.dhis.dxf2.importsummary.ImportStatus;
 import org.hisp.dhis.dxf2.importsummary.ImportSummary;
 import org.hisp.dhis.organisationunit.OrganisationUnit;
-import org.hisp.dhis.organisationunit.OrganisationUnitService;
 import org.hisp.dhis.period.Period;
 import org.hisp.dhis.period.PeriodType;
 import org.hisp.dhis.security.acl.AclService;
@@ -78,8 +77,6 @@ public class DataValueSetImportValidator {
 
   private final DataValueService dataValueService;
 
-  private final OrganisationUnitService organisationUnitService;
-
   /** Validation on the {@link DataSet} level */
   interface DataSetValidation {
     void validate(DataValueSet dataValueSet, ImportContext context, DataSetContext dataSetContext);
@@ -645,8 +642,7 @@ private void checkDataValueOrgUnitValidForAttrOptionCombo(
 
   private boolean isOrgUnitValidForAttrOptionCombo(DataValueContext valueContext) {
     Set<OrganisationUnit> aocOrgUnits = valueContext.getAttrOptionCombo().getOrganisationUnits();
-    return aocOrgUnits == null
-        || organisationUnitService.isDescendant(valueContext.getOrgUnit(), aocOrgUnits);
+    return aocOrgUnits == null || valueContext.getOrgUnit().isDescendant(aocOrgUnits);
   }
 
   private static void checkDataValueTargetDataSets(

dhis-2/dhis-services/dhis-service-dxf2/src/test/java/org/hisp/dhis/dxf2/datavalueset/DataValueSetImportValidatorTest.java

@@ -72,7 +72,6 @@
 import org.hisp.dhis.importexport.ImportStrategy;
 import org.hisp.dhis.option.OptionSet;
 import org.hisp.dhis.organisationunit.OrganisationUnit;
-import org.hisp.dhis.organisationunit.OrganisationUnitService;
 import org.hisp.dhis.period.Period;
 import org.hisp.dhis.period.PeriodType;
 import org.hisp.dhis.period.PeriodTypeEnum;
@@ -99,8 +98,6 @@ class DataValueSetImportValidatorTest {
 
   private DataValueSetImportValidator validator;
 
-  private OrganisationUnitService organisationUnitService;
-
   private final CategoryCombo defaultCombo = new CategoryCombo();
 
   @BeforeEach
@@ -109,16 +106,11 @@ void setUp() {
     lockExceptionStore = mock(LockExceptionStore.class);
     approvalService = mock(DataApprovalService.class);
     dataValueService = mock(DataValueService.class);
-    organisationUnitService = mock(OrganisationUnitService.class);
 
     i18n = mock(I18n.class);
     validator =
         new DataValueSetImportValidator(
-            aclService,
-            lockExceptionStore,
-            approvalService,
-            dataValueService,
-            organisationUnitService);
+            aclService, lockExceptionStore, approvalService, dataValueService);
     validator.init();
     setupUserCanWriteCategoryOptions(true);
     when(i18n.getString(anyString()))
@@ -298,12 +290,6 @@ void testValidateDataValueAttrOptionComboAccess() {
 
   @Test
   void testValidateDataValueOrgUnitInUserHierarchy() {
-    when(organisationUnitService.isDescendant(any(OrganisationUnit.class), any(Set.class)))
-        .thenReturn(false);
-    when(organisationUnitService.isDescendant(
-            any(OrganisationUnit.class), any(OrganisationUnit.class)))
-        .thenReturn(false);
-
     DataValue dataValue = createRandomDataValue();
     DataValueContext valueContext = createDataValueContext(dataValue).build();
     DataSetContext dataSetContext = createMinimalDataSetContext().build();

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

@@ -65,10 +65,6 @@
       <groupId>org.hisp.dhis.rules</groupId>
       <artifactId>rule-engine</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.springframework</groupId>
-      <artifactId>spring-core</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-jdbc</artifactId>
@@ -89,10 +85,6 @@
       <groupId>org.springframework</groupId>
       <artifactId>spring-beans</artifactId>
     </dependency>
-    <dependency>
-      <groupId>org.springframework.security</groupId>
-      <artifactId>spring-security-core</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.projectlombok</groupId>
       <artifactId>lombok</artifactId>