Merge branch 'master' into duplicate-cocs-prevent-import

dhis2 · Nov 27, 2024 · ab040db · ab040db
2 parents 9229d5e + 4e3c716
commit ab040db
Show file tree

Hide file tree

Showing 263 changed files with 3,842 additions and 3,121 deletions.
diff --git a/.github/workflows/run-api-tests.yml b/.github/workflows/run-api-tests.yml
@@ -41,13 +41,13 @@ jobs:
             # build and publish multi-arch images using Jib. Image is used for api tests in
             # this workflow and can be pulled from Dockerhub by devs to run locally, ...
             mvn clean verify --threads 2C --batch-mode --no-transfer-progress \
-              -DskipTests --update-snapshots --file dhis-2/pom.xml \
+              -DskipTests -Dmdep.analyze.skip --update-snapshots --file dhis-2/pom.xml \
               --projects dhis-web-server --also-make --activate-profiles jibBuild \
               -Djib.to.image=$CORE_IMAGE_NAME -Djib.container.labels=DHIS2_BUILD_REVISION=${{github.event.pull_request.head.sha}},DHIS2_BUILD_BRANCH=${{github.head_ref}}
           else
             # only build image for running api tests in this workflow i.e. master, 2.39, ...
             mvn clean verify --threads 2C --batch-mode --no-transfer-progress \
-              -DskipTests --update-snapshots --file dhis-2/pom.xml \
+              -DskipTests -Dmdep.analyze.skip --update-snapshots --file dhis-2/pom.xml \
               --projects dhis-web-server --also-make --activate-profiles jibDockerBuild \
               -Djib.to.image=$CORE_IMAGE_NAME
           fi

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -24,6 +24,9 @@ jobs:
       - name: Run unit tests
         run: mvn clean test --threads 2C --batch-mode --no-transfer-progress --update-snapshots --file ./dhis-2/pom.xml --activate-profiles unit-test
         timeout-minutes: 30
+      - name: Run dependency analysis
+        run: mvn dependency:analyze --file ./dhis-2/pom.xml
+        timeout-minutes: 2
       - name: Report coverage to codecov
         uses: codecov/codecov-action@v3
         with:

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryCombo.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryCombo.java
@@ -27,6 +27,7 @@
  */
 package org.hisp.dhis.category;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
@@ -195,6 +196,11 @@ public boolean hasOptionCombos() {
     return optionCombos != null && !optionCombos.isEmpty();
   }
 
+  @JsonIgnore
+  public List<Category> getDataDimensionCategories() {
+    return categories.stream().filter(Category::isDataDimension).toList();
+  }
+
   // -------------------------------------------------------------------------
   // Logic
   // -------------------------------------------------------------------------

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/DimensionalObjectUtils.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/DimensionalObjectUtils.java
@@ -141,7 +141,6 @@ public static DimensionalObject linkAssociations(
       EventAnalyticalObject eventAnalyticalObject,
       DimensionalObject dimensionalObject,
       Attribute parent) {
-    // Associating event repetitions.
     List<EventRepetition> repetitions = eventAnalyticalObject.getEventRepetitions();
 
     if (isNotEmpty(repetitions)) {

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/IdentifiableObjectManager.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/IdentifiableObjectManager.java
@@ -182,9 +182,6 @@ <T extends IdentifiableObject> List<T> getByCode(
   @CheckForNull
   <T extends IdentifiableObject> T search(@Nonnull Class<T> type, @Nonnull String query);
 
-  @Nonnull
-  <T extends IdentifiableObject> List<T> filter(@Nonnull Class<T> type, @Nonnull String query);
-
   @Nonnull
   <T extends IdentifiableObject> List<T> getAll(@Nonnull Class<T> type);
 

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/OpenApi.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/OpenApi.java
@@ -469,6 +469,7 @@ enum Status {
    */
   @Target(ElementType.TYPE)
   @Retention(RetentionPolicy.RUNTIME)
+  @Inherited
   @interface Shared {
 
     /**

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/collection/CollectionUtils.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/collection/CollectionUtils.java
@@ -214,6 +214,7 @@ private static <T> Set<T> union(@Nonnull Set<T>... more) {
    * @return a string, or null if no matches.
    */
   public static String popStartsWith(Collection<String> collection, String prefix) {
+    if (collection == null || collection.isEmpty()) return null;
     Iterator<String> iterator = collection.iterator();
 
     while (iterator.hasNext()) {

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/dashboard/embedded/EmbeddedDashboard.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/dashboard/embedded/EmbeddedDashboard.java
@@ -34,7 +34,11 @@
 import lombok.NoArgsConstructor;
 import lombok.Setter;
 
-/** Encapsulates metadata for an embedded and externally provided dashboard. */
+/**
+ * Encapsulates metadata for an embedded and externally provided dashboard.
+ *
+ * @author Lars Helge Overland
+ */
 @Getter
 @Setter
 @NoArgsConstructor

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/dashboard/embedded/FilterOptions.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/dashboard/embedded/FilterOptions.java
@@ -34,6 +34,11 @@
 import lombok.NoArgsConstructor;
 import lombok.Setter;
 
+/**
+ * Encapsulates embedded dashboard filter options.
+ *
+ * @author Lars Helge Overland
+ */
 @Getter
 @Setter
 @NoArgsConstructor

diff --git a/...a/org/hisp/dhis/fieldfilter/Defaults.java → ...a/org/hisp/dhis/fieldfilter/Defaults.java b/...a/org/hisp/dhis/fieldfilter/Defaults.java → ...a/org/hisp/dhis/fieldfilter/Defaults.java
diff --git a/...hisp/dhis/fieldfiltering/FieldPreset.java → ...hisp/dhis/fieldfiltering/FieldPreset.java b/...hisp/dhis/fieldfiltering/FieldPreset.java → ...hisp/dhis/fieldfiltering/FieldPreset.java
@@ -52,7 +52,7 @@ public enum FieldPreset {
 
   FieldPreset(String name, List<String> fields) {
     this.name = name;
-    this.fields = fields;
+    this.fields = List.copyOf(fields);
   }
 
   public String getName() {

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/interpretation/MentionUtils.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/interpretation/MentionUtils.java
@@ -31,7 +31,6 @@
 import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
-import java.util.ListIterator;
 import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -62,17 +61,4 @@ public static Set<User> getMentionedUsers(String text, UserService userService)
     }
     return users;
   }
-
-  public static List<String> removeCustomFilters(List<String> filters) {
-    List<String> mentions = new ArrayList<String>();
-    ListIterator<String> filterIterator = filters.listIterator();
-    while (filterIterator.hasNext()) {
-      String[] filterSplit = filterIterator.next().split(":");
-      if (filterSplit[1].equals("in") && filterSplit[0].equals("mentions")) {
-        mentions.add(filterSplit[2]);
-        filterIterator.remove();
-      }
-    }
-    return mentions;
-  }
 }
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/message/MessageConversation.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/message/MessageConversation.java
@@ -41,6 +41,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.hisp.dhis.common.BaseIdentifiableObject;
 import org.hisp.dhis.common.DxfNamespaces;
+import org.hisp.dhis.common.UID;
 import org.hisp.dhis.schema.annotation.PropertyRange;
 import org.hisp.dhis.user.User;
 
@@ -192,12 +193,12 @@ public boolean isRead(User user) {
     return false;
   }
 
-  public boolean markRead(User user) {
-    for (UserMessage userMessage : userMessages) {
-      if (userMessage.getUser() != null && userMessage.getUser().equals(user)) {
-        boolean read = userMessage.isRead();
+  public boolean markRead(UID user) {
+    for (UserMessage msg : userMessages) {
+      if (msg.getUser() != null && msg.getUser().getUid().equals(user.getValue())) {
+        boolean read = msg.isRead();
 
-        userMessage.setRead(true);
+        msg.setRead(true);
 
         return !read;
       }

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/organisationunit/OrganisationUnitService.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/organisationunit/OrganisationUnitService.java
@@ -133,14 +133,6 @@ public interface OrganisationUnitService extends OrganisationUnitDataIntegrityPr
    */
   List<OrganisationUnit> getOrganisationUnitsByUid(@Nonnull Collection<String> uids);
 
-  /**
-   * Returns a list of OrganisationUnits based on the given params.
-   *
-   * @param params the params.
-   * @return a list of OrganisationUnits.
-   */
-  List<OrganisationUnit> getOrganisationUnitsByQuery(OrganisationUnitQueryParams params);
-
   /**
    * Returns an OrganisationUnit with a given name.
    *

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserDetails.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserDetails.java
@@ -28,6 +28,7 @@
 package org.hisp.dhis.user;
 
 import java.util.Collection;
+import java.util.List;
 import java.util.Objects;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -250,6 +251,14 @@ static UserDetails createUserDetails(
 
   void setId(Long id);
 
+  default boolean canIssueUserRole(UserRole role, boolean canGrantOwnUserRole) {
+    if (role == null) return false;
+    if (isSuper()) return true;
+    if (hasAnyAuthorities(List.of(Authorities.ALL))) return true;
+    if (!canGrantOwnUserRole && getUserRoleIds().contains(role.getUid())) return false;
+    return getAllAuthorities().containsAll(role.getAuthorities());
+  }
+
   default boolean isInUserHierarchy(String orgUnitPath) {
     return isInUserHierarchy(orgUnitPath, getUserOrgUnitIds());
   }

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserService.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserService.java
@@ -43,6 +43,7 @@
 import org.hisp.dhis.common.IdentifiableObject;
 import org.hisp.dhis.common.UID;
 import org.hisp.dhis.dataset.DataSet;
+import org.hisp.dhis.feedback.ConflictException;
 import org.hisp.dhis.feedback.ErrorCode;
 import org.hisp.dhis.feedback.ErrorReport;
 import org.hisp.dhis.feedback.ForbiddenException;
@@ -235,6 +236,17 @@ static boolean hasTwoFactorSecretForApproval(User user) {
    */
   List<User> getUsers(UserQueryParams params, @Nullable List<String> orders);
 
+  /**
+   * Returns a list of users based on the given query parameters. If the specified list of orders
+   * are empty, default order of last name and first name will be applied.
+   *
+   * @param params the user query parameters.
+   * @param orders the already validated order strings (e.g. email:asc).
+   * @return a List of users.
+   */
+  List<UID> getUserIds(UserQueryParams params, @Nullable List<String> orders)
+      throws ConflictException;
+
   /**
    * Returns the number of users based on the given query parameters.
    *
@@ -408,12 +420,9 @@ static boolean hasTwoFactorSecretForApproval(User user) {
   int countDataSetUserRoles(DataSet dataSet);
 
   /**
-   * Filters the given collection of user roles based on whether the current user is allowed to
-   * issue it.
-   *
-   * @param userRoles the collection of user roles.
+   * @return IDs of the roles the current user can issue
    */
-  void canIssueFilter(Collection<UserRole> userRoles);
+  List<UID> getRolesCurrentUserCanIssue();
 
   /**
    * Validate that the current user are allowed to create or modify properties of the given user.

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserStore.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserStore.java
@@ -65,6 +65,8 @@ public interface UserStore extends IdentifiableObjectStore<User> {
    */
   List<User> getUsers(UserQueryParams params, @Nullable List<String> orders);
 
+  List<UID> getUserIds(UserQueryParams params, @Nullable List<String> orders);
+
   /**
    * Returns the number of users based on the given query parameters.
    *

diff --git a/dhis-2/dhis-services/dhis-service-administration/pom.xml b/dhis-2/dhis-services/dhis-service-administration/pom.xml
@@ -131,7 +131,7 @@
     <dependency>
       <groupId>com.networknt</groupId>
       <artifactId>json-schema-validator</artifactId>
-      <version>1.5.3</version>
+      <version>1.5.4</version>
       <exclusions>
         <exclusion>
           <groupId>org.apache.commons</groupId>

diff --git a/...es/dhis-service-analytics/src/main/java/org/hisp/dhis/analytics/config/ServiceConfig.java b/...es/dhis-service-analytics/src/main/java/org/hisp/dhis/analytics/config/ServiceConfig.java
@@ -27,18 +27,31 @@
  */
 package org.hisp.dhis.analytics.config;
 
+import org.hisp.dhis.analytics.AnalyticsTableHookService;
 import org.hisp.dhis.analytics.AnalyticsTableManager;
 import org.hisp.dhis.analytics.AnalyticsTableService;
+import org.hisp.dhis.analytics.partition.PartitionManager;
 import org.hisp.dhis.analytics.table.DefaultAnalyticsTableService;
+import org.hisp.dhis.analytics.table.JdbcTrackedEntityEventsAnalyticsTableManager;
+import org.hisp.dhis.analytics.table.setting.AnalyticsTableSettings;
+import org.hisp.dhis.category.CategoryService;
+import org.hisp.dhis.common.IdentifiableObjectManager;
+import org.hisp.dhis.dataapproval.DataApprovalLevelService;
 import org.hisp.dhis.dataelement.DataElementService;
+import org.hisp.dhis.db.sql.AnalyticsSqlBuilder;
+import org.hisp.dhis.db.sql.AnalyticsSqlBuilderProvider;
 import org.hisp.dhis.db.sql.SqlBuilder;
 import org.hisp.dhis.db.sql.SqlBuilderProvider;
 import org.hisp.dhis.organisationunit.OrganisationUnitService;
+import org.hisp.dhis.period.PeriodDataProvider;
 import org.hisp.dhis.resourcetable.ResourceTableService;
 import org.hisp.dhis.setting.SystemSettingsProvider;
+import org.hisp.dhis.system.database.DatabaseInfoProvider;
+import org.hisp.dhis.trackedentity.TrackedEntityTypeService;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.jdbc.core.JdbcTemplate;
 
 /**
  * @author Luciano Fiandesio
@@ -50,6 +63,46 @@ public SqlBuilder sqlBuilder(SqlBuilderProvider provider) {
     return provider.getSqlBuilder();
   }
 
+  @Bean
+  public AnalyticsSqlBuilder analyticsSqlBuilder(AnalyticsSqlBuilderProvider provider) {
+    return provider.getAnalyticsSqlBuilder();
+  }
+
+  @Bean("org.hisp.dhis.analytics.TrackedEntityEventsAnalyticsTableManager")
+  public AnalyticsTableManager jdbcTrackedEntityEventsAnalyticsTableManager(
+      IdentifiableObjectManager idObjectManager,
+      OrganisationUnitService organisationUnitService,
+      CategoryService categoryService,
+      SystemSettingsProvider settingsProvider,
+      DataApprovalLevelService dataApprovalLevelService,
+      ResourceTableService resourceTableService,
+      AnalyticsTableHookService tableHookService,
+      PartitionManager partitionManager,
+      DatabaseInfoProvider databaseInfoProvider,
+      @Qualifier("analyticsJdbcTemplate") JdbcTemplate jdbcTemplate,
+      TrackedEntityTypeService trackedEntityTypeService,
+      AnalyticsTableSettings analyticsTableSettings,
+      PeriodDataProvider periodDataProvider,
+      SqlBuilder sqlBuilder,
+      AnalyticsSqlBuilder analyticsSqlBuilder) {
+    return new JdbcTrackedEntityEventsAnalyticsTableManager(
+        idObjectManager,
+        organisationUnitService,
+        categoryService,
+        settingsProvider,
+        dataApprovalLevelService,
+        resourceTableService,
+        tableHookService,
+        partitionManager,
+        databaseInfoProvider,
+        jdbcTemplate,
+        trackedEntityTypeService,
+        analyticsTableSettings,
+        periodDataProvider,
+        sqlBuilder,
+        analyticsSqlBuilder);
+  }
+
   @Bean("org.hisp.dhis.analytics.TrackedEntityAnalyticsTableService")
   public AnalyticsTableService trackedEntityAnalyticsTableManager(
       @Qualifier("org.hisp.dhis.analytics.TrackedEntityAnalyticsTableManager")

diff --git a/...service-analytics/src/main/java/org/hisp/dhis/analytics/data/DefaultDataQueryService.java b/...service-analytics/src/main/java/org/hisp/dhis/analytics/data/DefaultDataQueryService.java
@@ -93,7 +93,7 @@
 @Service("org.hisp.dhis.analytics.DataQueryService")
 @RequiredArgsConstructor
 public class DefaultDataQueryService implements DataQueryService {
-  private final DimensionalObjectProducer dimensionalObjectProducer;
+  private final DimensionalObjectProvider dimensionalObjectProducer;
 
   private final IdentifiableObjectManager idObjectManager;
 

diff --git a/...ytics/data/DimensionalObjectProducer.java → ...ytics/data/DimensionalObjectProvider.java b/...ytics/data/DimensionalObjectProducer.java → ...ytics/data/DimensionalObjectProvider.java
@@ -116,7 +116,7 @@
  */
 @Component
 @RequiredArgsConstructor
-public class DimensionalObjectProducer {
+public class DimensionalObjectProvider {
   private final IdentifiableObjectManager idObjectManager;
 
   private final OrganisationUnitService organisationUnitService;

diff --git a/...vice-analytics/src/main/java/org/hisp/dhis/analytics/outlier/data/OutlierQueryParser.java b/...vice-analytics/src/main/java/org/hisp/dhis/analytics/outlier/data/OutlierQueryParser.java
@@ -39,7 +39,7 @@
 import java.util.UUID;
 import lombok.AllArgsConstructor;
 import org.apache.commons.lang3.StringUtils;
-import org.hisp.dhis.analytics.data.DimensionalObjectProducer;
+import org.hisp.dhis.analytics.data.DimensionalObjectProvider;
 import org.hisp.dhis.category.CategoryOptionCombo;
 import org.hisp.dhis.common.BaseDimensionalObject;
 import org.hisp.dhis.common.DisplayProperty;
@@ -60,7 +60,7 @@
 @AllArgsConstructor
 public class OutlierQueryParser {
   private final IdentifiableObjectManager idObjectManager;
-  private final DimensionalObjectProducer dimensionalObjectProducer;
+  private final DimensionalObjectProvider dimensionalObjectProducer;
   private final UserService userService;
 
   /**

diff --git a/...lytics/src/main/java/org/hisp/dhis/analytics/outlier/service/AnalyticsOutlierService.java b/...lytics/src/main/java/org/hisp/dhis/analytics/outlier/service/AnalyticsOutlierService.java
@@ -63,7 +63,7 @@
 import org.hisp.dhis.analytics.cache.OutliersCache;
 import org.hisp.dhis.analytics.common.ColumnHeader;
 import org.hisp.dhis.analytics.common.TableInfoReader;
-import org.hisp.dhis.analytics.data.DimensionalObjectProducer;
+import org.hisp.dhis.analytics.data.DimensionalObjectProvider;
 import org.hisp.dhis.analytics.outlier.data.Outlier;
 import org.hisp.dhis.analytics.outlier.data.OutlierRequest;
 import org.hisp.dhis.category.CategoryOptionCombo;
@@ -104,7 +104,7 @@ public class AnalyticsOutlierService {
 
   private final IdentifiableObjectManager idObjectManager;
 
-  private final DimensionalObjectProducer dimensionalObjectProducer;
+  private final DimensionalObjectProvider dimensionalObjectProducer;
 
   /**
    * Transform the incoming request into api response (json).