Merge branch 'master' into DHIS2-18239

.github/workflows/analyse-pr.yml

@@ -20,6 +20,7 @@ concurrency:
   cancel-in-progress: true
 jobs:
   sonarqube:
+    if: github.actor != 'dependabot[bot]'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -38,13 +39,13 @@ jobs:
           BASE_BRANCH: ${{ github.base_ref }}
           BRANCH: ${{ github.ref }}
           PR: ${{ github.event.number }}
-        if: github.event_name == 'pull_request'
+        if: github.event.pull_request.user.login != 'dependabot[bot]' && github.event_name == 'pull_request'
         run: |
           mvn -f dhis-2/pom.xml clean install --threads 2C --batch-mode --update-snapshots --no-transfer-progress -DskipTests
           mvn -f dhis-2/pom.xml sonar:sonar -Dsonar.internal.analysis.dbd=false --batch-mode --no-transfer-progress -Dsonar.scm.revision=${{ github.event.pull_request.head.sha }} -Dsonar.projectKey=dhis2_dhis2-core
 
       - name: Analyse long-living branch
-        if: github.event_name != 'pull_request'
+        if: github.event.pull_request.user.login != 'dependabot[bot]' && github.event_name != 'pull_request'
         run: |
           mvn -f dhis-2/pom.xml clean install --threads 2C --batch-mode --update-snapshots --no-transfer-progress -DskipTests
           mvn -f dhis-2/pom.xml sonar:sonar -Dsonar.internal.analysis.dbd=false --batch-mode --no-transfer-progress -Dsonar.branch.name=${GITHUB_REF#refs/heads/} -Dsonar.projectKey=dhis2_dhis2-core

.github/workflows/codeql-analysis.yml

@@ -13,12 +13,13 @@ on:
     branches:
       - master
   schedule:
-    - cron: '0 12 * * *'
+    - cron: "0 12 * * *"
 concurrency:
-    group: ${{ github.workflow}}-${{ github.ref }}
-    cancel-in-progress: true
+  group: ${{ github.workflow}}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   analyze:
+    if: github.actor != 'dependabot[bot]'
     name: Analyze
     runs-on: ubuntu-latest
 
@@ -27,7 +28,7 @@ jobs:
       matrix:
         # Override automatic language detection by changing the below list
         # Supported options are ['csharp', 'cpp', 'go', 'java', 'javascript', 'python']
-        language: [ 'java' ]
+        language: ["java"]
         # Learn more...
         # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
 

dhis-2/dhis-api/src/main/java/org/hisp/dhis/analytics/CategoryDimensionStore.java

@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2004-2024, 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.analytics;
+
+import java.util.Collection;
+import java.util.List;
+import org.hisp.dhis.category.CategoryDimension;
+import org.hisp.dhis.category.CategoryOption;
+import org.hisp.dhis.common.GenericStore;
+
+/**
+ * @author david mackessy
+ */
+public interface CategoryDimensionStore extends GenericStore<CategoryDimension> {
+
+  /**
+   * Gets all {@link CategoryDimension}s that reference any of the supplied {@link CategoryOption}s
+   *
+   * @param categoryOptions to search for
+   * @return matching {@link CategoryDimension}s
+   */
+  List<CategoryDimension> getByCategoryOption(Collection<String> categoryOptions);
+}

dhis-2/dhis-api/src/main/java/org/hisp/dhis/cache/SoftCache.java

@@ -0,0 +1,95 @@
+/*
+ * Copyright (c) 2004-2024, 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.cache;
+
+import java.lang.ref.SoftReference;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import java.util.function.Supplier;
+import javax.annotation.CheckForNull;
+import javax.annotation.Nonnull;
+
+/**
+ * A soft cache uses a concurrent map with {@link java.lang.ref.SoftReference} boxed values.
+ *
+ * <p>This means the values might get GC-ed if the JVM needs memory. Therefore, when accessing a
+ * value by key, a {@link java.util.function.Supplier} needs to be passed in case the value needs
+ * re-computing.
+ *
+ * @author Jan Bernitt
+ * @since 2.42
+ */
+public final class SoftCache<T> {
+
+  private final ConcurrentMap<String, SoftReference<T>> cache = new ConcurrentHashMap<>();
+
+  /**
+   * Access a cached value by key.
+   *
+   * @param key the key to get from the cache, when null the value is computed and not cached
+   * @param onMiss a function to compute the value on a cache miss; the function must not return
+   *     null
+   * @return the cached or computed value
+   */
+  @Nonnull
+  public T get(@CheckForNull String key, @Nonnull Supplier<T> onMiss) {
+    if (key == null) return onMiss.get();
+    Supplier<T> memOnMiss = memorize(onMiss);
+    T res =
+        cache
+            .compute(
+                key,
+                (k, v) -> {
+                  if (v == null) return new SoftReference<>(memOnMiss.get());
+                  if (v.get() != null) return v;
+                  return new SoftReference<>(memOnMiss.get());
+                })
+            .get();
+    // in theory the get() of the SoftReference can become null
+    // just when it is returned from the map
+    // in which case the res is taken directly from the supplier
+    // since this should mean the JVM is low on memory
+    return res == null ? memOnMiss.get() : res;
+  }
+
+  /**
+   * @param onMiss assumed expensive to compute
+   * @return a supplier that will memorize the result once it has been computed
+   */
+  private Supplier<T> memorize(Supplier<T> onMiss) {
+    Object[] memorize = new Object[1];
+    return () -> {
+      @SuppressWarnings("unchecked")
+      T v = (T) memorize[0];
+      if (v != null) return v;
+      v = onMiss.get();
+      memorize[0] = v;
+      return v;
+    };
+  }
+}

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/Category.java

@@ -34,6 +34,7 @@
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
 import com.google.common.collect.Lists;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -92,6 +93,10 @@ public void removeCategoryOption(CategoryOption categoryOption) {
     categoryOption.getCategories().remove(this);
   }
 
+  public void removeCategoryOptions(Collection<CategoryOption> categoryOptions) {
+    categoryOptions.forEach(this::removeCategoryOption);
+  }
+
   public void removeAllCategoryOptions() {
     for (CategoryOption categoryOption : categoryOptions) {
       categoryOption.getCategories().remove(this);

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryDimension.java

@@ -33,7 +33,9 @@
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
+import javax.annotation.Nonnull;
 import org.hisp.dhis.common.BaseIdentifiableObject;
 import org.hisp.dhis.common.DimensionalEmbeddedObject;
 import org.hisp.dhis.common.DxfNamespaces;
@@ -83,6 +85,18 @@ public void setItems(List<CategoryOption> items) {
     this.items = items;
   }
 
+  public void addItem(CategoryOption item) {
+    this.getItems().add(item);
+  }
+
+  public void removeItem(CategoryOption item) {
+    this.getItems().remove(item);
+  }
+
+  public void removeItems(@Nonnull Collection<CategoryOption> items) {
+    items.forEach(this::removeItem);
+  }
+
   @Override
   public String toString() {
     final StringBuilder sb = new StringBuilder("CategoryDimension{");

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryOption.java

@@ -32,6 +32,7 @@
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import java.util.Collection;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.Set;
@@ -116,11 +117,19 @@ public void addCategoryOptionCombo(CategoryOptionCombo dataElementCategoryOption
     dataElementCategoryOptionCombo.getCategoryOptions().add(this);
   }
 
+  public void addCategoryOptionCombos(Collection<CategoryOptionCombo> categoryOptionCombos) {
+    categoryOptionCombos.forEach(this::addCategoryOptionCombo);
+  }
+
   public void removeCategoryOptionCombo(CategoryOptionCombo dataElementCategoryOptionCombo) {
     categoryOptionCombos.remove(dataElementCategoryOptionCombo);
     dataElementCategoryOptionCombo.getCategoryOptions().remove(this);
   }
 
+  public void removeCategoryOptionCombos(Collection<CategoryOptionCombo> categoryOptionCombos) {
+    categoryOptionCombos.forEach(this::removeCategoryOptionCombo);
+  }
+
   public void addOrganisationUnit(OrganisationUnit organisationUnit) {
     organisationUnits.add(organisationUnit);
     organisationUnit.getCategoryOptions().add(this);

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryOptionCombo.java

@@ -33,6 +33,7 @@
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import java.util.Collection;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
@@ -151,6 +152,10 @@ public void removeCategoryOption(CategoryOption dataElementCategoryOption) {
     dataElementCategoryOption.getCategoryOptionCombos().remove(this);
   }
 
+  public void removeCategoryOptions(Collection<CategoryOption> categoryOptions) {
+    categoryOptions.forEach(this::removeCategoryOption);
+  }
+
   public void removeAllCategoryOptions() {
     categoryOptions.clear();
   }

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryOptionComboStore.java

@@ -27,6 +27,7 @@
  */
 package org.hisp.dhis.category;
 
+import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 import org.hisp.dhis.common.IdentifiableObjectStore;
@@ -56,4 +57,13 @@ CategoryOptionCombo getCategoryOptionCombo(
    * @return a List of {@link CategoryOptionCombo} or empty List
    */
   List<CategoryOptionCombo> getCategoryOptionCombosByGroupUid(String groupId, String dataElementId);
+
+  /**
+   * Retrieves all CategoryOptionCombos with a ref to any of the CategoryOptions passed in.
+   *
+   * @param categoryOptions refs to search for
+   * @return categoryOptionCombos with refs to categoryOptions
+   */
+  List<CategoryOptionCombo> getCategoryOptionCombosByCategoryOption(
+      Collection<String> categoryOptions);
 }

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryOptionGroup.java

@@ -32,6 +32,7 @@
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
 import org.hisp.dhis.common.BaseDimensionalItemObject;
@@ -128,4 +129,8 @@ public void removeCategoryOption(CategoryOption categoryOption) {
     members.remove(categoryOption);
     categoryOption.getGroups().remove(this);
   }
+
+  public void removeCategoryOptions(Collection<CategoryOption> categoryOptions) {
+    categoryOptions.forEach(this::removeCategoryOption);
+  }
 }

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryOptionGroupStore.java

@@ -27,9 +27,12 @@
  */
 package org.hisp.dhis.category;
 
+import java.util.Collection;
 import java.util.List;
 import org.hisp.dhis.common.IdentifiableObjectStore;
 
 public interface CategoryOptionGroupStore extends IdentifiableObjectStore<CategoryOptionGroup> {
   List<CategoryOptionGroup> getCategoryOptionGroups(CategoryOptionGroupSet groupSet);
+
+  List<CategoryOptionGroup> getByCategoryOption(Collection<String> categoryOptions);
 }

dhis-2/dhis-api/src/main/java/org/hisp/dhis/category/CategoryService.java

@@ -32,6 +32,7 @@
 import java.util.Set;
 import org.apache.commons.collections4.SetValuedMap;
 import org.hisp.dhis.common.IdScheme;
+import org.hisp.dhis.common.UID;
 import org.hisp.dhis.dataelement.DataElement;
 import org.hisp.dhis.dataelement.DataElementOperand;
 import org.hisp.dhis.dataset.DataSet;
@@ -145,6 +146,14 @@ public interface CategoryService {
    */
   List<Category> getAttributeDataDimensionCategoriesNoAcl();
 
+  /**
+   * Retrieves all Categories with a ref to any of the CategoryOptions passed in.
+   *
+   * @param categoryOptions refs to search for
+   * @return categories with refs to categoryOptions
+   */
+  List<Category> getCategoriesByCategoryOption(Collection<UID> categoryOptions);
+
   // -------------------------------------------------------------------------
   // CategoryOption
   // -------------------------------------------------------------------------
@@ -461,6 +470,15 @@ CategoryOptionCombo getCategoryOptionCombo(
   /** Updates the name property of all category option combinations. */
   void updateCategoryOptionComboNames();
 
+  /**
+   * Retrieves all CategoryOptionCombos with a ref to any of the CategoryOptions passed in.
+   *
+   * @param categoryOptions refs to search for
+   * @return categoryOptionCombos with refs to categoryOptions
+   */
+  List<CategoryOptionCombo> getCategoryOptionCombosByCategoryOption(
+      Collection<UID> categoryOptions);
+
   // -------------------------------------------------------------------------
   // DataElementOperand
   // -------------------------------------------------------------------------
@@ -509,6 +527,8 @@ CategoryOptionCombo getCategoryOptionCombo(
 
   List<CategoryOptionGroup> getCategoryOptionGroups(CategoryOptionGroupSet groupSet);
 
+  List<CategoryOptionGroup> getCategoryOptionGroupByCategoryOption(Collection<UID> categoryOptions);
+
   /**
    * Returns a set of CategoryOptionGroups that may be seen by the current user, if the current user
    * has any CategoryOptionGroupSet constraint(s).
@@ -541,4 +561,6 @@ CategoryOptionCombo getCategoryOptionCombo(
   CategoryOption getDefaultCategoryOption();
 
   Category getDefaultCategory();
+
+  List<CategoryOption> getCategoryOptionsByUid(List<String> catOptionUids);
 }