Merge branch 'master' into DHIS2-16960_2.42

dhis2 · Dec 26, 2024 · c3e476d · c3e476d
2 parents 6341342 + a7dc1d0
commit c3e476d
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -52,12 +52,6 @@ updates:
       - dependency-name: "org.springframework.ldap:*" # Spring ldap 3.x requires Spring 6 (see above)
         versions:
           - ">= 3.0"
-      - dependency-name: "org.hisp.dhis.parser:*" # Antlr parser must be upgraded manually due to circular dependency with rule engine
-        versions:
-          - ">= 1.0"
-      - dependency-name: "org.hisp.dhis.rules:*" # Rule engine must be upgraded manually due to circular dependency with ANTLR parser
-        versions:
-          - ">= 2.0"
       - dependency-name: "org.slf4j:slf4j-api" # will update in https://dhis2.atlassian.net/browse/DHIS2-16504
         versions:
           - ">= 2.0"
@@ -138,12 +132,6 @@ updates:
       - dependency-name: "org.springframework.ldap:*" # Spring ldap 3.x requires Spring 6 (see above)
         versions:
           - ">= 3.0"
-      - dependency-name: "org.hisp.dhis.parser:*" # Antlr parser must be upgraded manually due to circular dependency with rule engine
-        versions:
-          - ">= 1.0"
-      - dependency-name: "org.hisp.dhis.rules:*" # Rule engine must be upgraded manually due to circular dependency with ANTLR parser
-        versions:
-          - ">= 2.0"
       - dependency-name: "org.flywaydb:flyway-core" # It requires Postgres version to be >= 11
         versions:
           - "> 9.22.3"

diff --git a/.github/workflows/generate-merge-boms.yml b/.github/workflows/generate-merge-boms.yml
@@ -0,0 +1,51 @@
+name: Generate and Merge SBOMs and Upload them to DependencyTrack every night
+
+on:
+  schedule:
+    - cron: "0 0 * * *" # Run every day at midnight
+
+concurrency:
+  group: ${{ github.workflow}}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  create-boms:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: dhis-2/
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          fetch-depth: 0
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: 17
+          distribution: temurin
+          cache: maven
+
+      - name: Install CycloneDX CLI
+        run: |
+          curl -s https://api.github.com/repos/CycloneDX/cyclonedx-cli/releases/latest | grep "browser_download_url.*linux.x64" | cut -d '"' -f 4 | wget -i -
+          sudo mv cyclonedx-linux-x64 /usr/local/bin/
+          sudo chmod +x /usr/local/bin/cyclonedx-linux-x64
+
+      - name: Generate BOMs
+        run: mvn cyclonedx:makeBom
+
+      - name: Merge BOMs
+        run: cyclonedx-linux-x64 merge --input-files $(find . -name 'dxbom.json') --input-format json --output-file target/merged-bom.json --output-format json
+
+      - name: Upload SBOM to DependencyTrack
+        env:
+          DEPENDENCY_TRACK_API: "https://dt.security.dhis2.org/api/v1/bom"
+        run: |
+          curl -X POST "$DEPENDENCY_TRACK_API" \
+              --fail-with-body \
+              -H "Content-Type: multipart/form-data" \
+              -H "X-Api-Key: ${{ secrets.DEPENDENCYTRACK_APIKEY }}" \
+              -F "project=56383704-d5a2-4a35-ad6a-081f80f5d6d3" \
+              -F "bom=@target/merged-bom.json"
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/DataDimensionItem.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/DataDimensionItem.java
@@ -27,6 +27,8 @@
  */
 package org.hisp.dhis.common;
 
+import static org.hisp.dhis.analytics.Aggregation.AGGREGATED;
+
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
@@ -40,6 +42,7 @@
 import java.util.stream.Collectors;
 import lombok.AllArgsConstructor;
 import lombok.NoArgsConstructor;
+import org.hisp.dhis.analytics.Aggregation;
 import org.hisp.dhis.dataelement.DataElement;
 import org.hisp.dhis.dataelement.DataElementOperand;
 import org.hisp.dhis.expressiondimensionitem.ExpressionDimensionItem;
@@ -113,16 +116,31 @@ public class DataDimensionItem {
   @AllArgsConstructor
   public static class Attributes implements Serializable {
     /** The option item for this dimension item. * */
-    private OptionSetItem optionItem;
+    private OptionSetItem optionSetItem;
 
     @JsonProperty
     @JacksonXmlProperty(namespace = DxfNamespaces.DXF_2_0)
     public OptionSetItem getOptionSetItem() {
-      return optionItem;
+      return optionSetItem;
+    }
+
+    /**
+     * This method ensure that existing persisted items will return default values, case the current
+     * {@link OptionSetItem} is null or does not have an {@link Aggregation} defined.
+     *
+     * @return the correct version of an {@link OptionSetItem}.
+     */
+    public OptionSetItem getOptionSetItemOrDefault() {
+      if (optionSetItem != null) {
+        return new OptionSetItem(
+            optionSetItem.getOptions(), optionSetItem.getAggregationOrDefault());
+      }
+
+      return new OptionSetItem(Set.of(), AGGREGATED);
     }
 
-    public void setOptionSetItem(OptionSetItem optionItem) {
-      this.optionItem = optionItem;
+    public void setOptionSetItem(OptionSetItem optionSetItem) {
+      this.optionSetItem = optionSetItem;
     }
   }
 
@@ -232,14 +250,17 @@ public DimensionalItemObject getDimensionalItemObject() {
   }
 
   /**
-   * Simply loads the internal attributes into the given item object.
+   * Simply loads the internal attributes into the given item object. Some objects, when null, will
+   * be loaded with their respective defaults.
    *
    * @param itemObject the {@link BaseDimensionalItemObject}.
    */
   private void loadAttributes(BaseDimensionalItemObject itemObject) {
-    if (attributes != null) {
-      itemObject.setOptionSetItem(attributes.getOptionSetItem());
+    if (attributes == null) {
+      attributes = new Attributes();
     }
+
+    itemObject.setOptionSetItem(attributes.getOptionSetItemOrDefault());
   }
 
   @JsonProperty

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/OptionSetItem.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/OptionSetItem.java
@@ -27,6 +27,7 @@
  */
 package org.hisp.dhis.common;
 
+import static org.hisp.dhis.analytics.Aggregation.AGGREGATED;
 import static org.hisp.dhis.common.DxfNamespaces.DXF_2_0;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -71,4 +72,17 @@ public Aggregation getAggregation() {
   public void setAggregation(Aggregation aggregation) {
     this.aggregation = aggregation;
   }
+
+  /**
+   * Returns the current {@link Aggregation} or default.
+   *
+   * @return the respective {@link Aggregation} object.
+   */
+  public Aggregation getAggregationOrDefault() {
+    if (aggregation == null) {
+      return AGGREGATED;
+    }
+
+    return aggregation;
+  }
 }
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/dataitem/DataItem.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/dataitem/DataItem.java
@@ -100,6 +100,10 @@ public class DataItem implements Serializable {
   @JacksonXmlProperty(namespace = DXF_2_0)
   private String expression;
 
+  @JsonProperty
+  @JacksonXmlProperty(namespace = DXF_2_0)
+  private String optionSetId;
+
   public ValueType getSimplifiedValueType() {
     return valueType != null ? valueType.toSimplifiedValueType() : null;
   }

diff --git a/...rvices/dhis-service-core/src/main/java/org/hisp/dhis/dataitem/query/DataElementQuery.java b/...rvices/dhis-service-core/src/main/java/org/hisp/dhis/dataitem/query/DataElementQuery.java
@@ -27,6 +27,7 @@
  */
 package org.hisp.dhis.dataitem.query;
 
+import static java.util.stream.Collectors.joining;
 import static java.util.stream.Collectors.toSet;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.hisp.dhis.common.ValueType.getAggregatables;
@@ -37,6 +38,7 @@
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.ifAny;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.ifSet;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.nameFiltering;
+import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.optionSetIdFiltering;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.rootJunction;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.shortNameFiltering;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.uidFiltering;
@@ -54,8 +56,10 @@
 import static org.hisp.dhis.dataitem.query.shared.UserAccessStatement.READ_ACCESS;
 import static org.hisp.dhis.dataitem.query.shared.UserAccessStatement.sharingConditions;
 
+import java.util.List;
 import java.util.Set;
 import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.lang3.tuple.Pair;
 import org.hisp.dhis.common.BaseIdentifiableObject;
 import org.hisp.dhis.dataitem.query.shared.OptionalFilterBuilder;
 import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
@@ -70,12 +74,28 @@
 @Component
 public class DataElementQuery implements DataItemQuery {
   private static final String COMMON_COLUMNS =
-      "cast (null as text) as program_name, cast (null as text) as program_uid,"
-          + " cast (null as text) as program_shortname, dataelement.uid as item_uid, dataelement.name as item_name,"
-          + " dataelement.shortname as item_shortname, dataelement.valuetype as item_valuetype,"
-          + " dataelement.code as item_code, dataelement.sharing as item_sharing, dataelement.domaintype as item_domaintype,"
-          + " cast ('DATA_ELEMENT' as text) as item_type,"
-          + " cast (null as text) as expression";
+      List.of(
+              Pair.of("program_name", CAST_NULL_AS_TEXT),
+              Pair.of("program_uid", CAST_NULL_AS_TEXT),
+              Pair.of("program_shortname", CAST_NULL_AS_TEXT),
+              Pair.of("item_uid", "dataelement.uid"),
+              Pair.of("item_name", "dataelement.name"),
+              Pair.of("item_shortname", "dataelement.shortname"),
+              Pair.of("item_valuetype", "dataelement.valuetype"),
+              Pair.of("item_code", "dataelement.code"),
+              Pair.of("item_sharing", "dataelement.sharing"),
+              Pair.of("item_domaintype", "dataelement.domaintype"),
+              Pair.of("item_type", "cast ('DATA_ELEMENT' as text)"),
+              Pair.of("expression", CAST_NULL_AS_TEXT),
+              Pair.of("optionset_uid", "optionset.uid"))
+          .stream()
+          .map(pair -> pair.getRight() + " as " + pair.getLeft())
+          .collect(joining(", "));
+
+  private static final String JOINS =
+      "left join optionset on dataelement.optionsetid = optionset.optionsetid";
+
+  private static final String SPACED_FROM_DATA_ELEMENT = " from dataelement ";
 
   @Override
   public String getStatement(MapSqlParameterSource paramsMap) {
@@ -95,7 +115,7 @@ public String getStatement(MapSqlParameterSource paramsMap) {
     }
 
     sql.append(
-        " group by item_name, item_uid, item_valuetype, item_code, item_domaintype, item_sharing, item_shortname,"
+        " group by optionset.uid, item_name, item_uid, item_valuetype, item_code, item_domaintype, item_sharing, item_shortname,"
             + " i18n_first_name, i18n_first_shortname, i18n_second_name, i18n_second_shortname");
 
     // Closing the temp table.
@@ -131,6 +151,7 @@ public String getStatement(MapSqlParameterSource paramsMap) {
     optionalFilters.append(ifSet(nameFiltering("t.item_name", paramsMap)));
     optionalFilters.append(ifSet(shortNameFiltering("t.item_shortname", paramsMap)));
     optionalFilters.append(ifSet(uidFiltering("t.item_uid", paramsMap)));
+    optionalFilters.append(ifSet(optionSetIdFiltering("t.optionset_uid", paramsMap)));
     sql.append(ifAny(optionalFilters.toString()));
 
     String identifiableStatement =
@@ -180,9 +201,11 @@ public Class<? extends BaseIdentifiableObject> getRootEntity() {
   private String selectRowsContainingTranslatedName() {
     StringBuilder sql = new StringBuilder();
 
-    sql.append(SPACED_SELECT + COMMON_COLUMNS).append(translationNamesColumnsFor("dataelement"));
-
-    sql.append(" from dataelement ").append(translationNamesJoinsOn("dataelement"));
+    sql.append(SPACED_SELECT + COMMON_COLUMNS)
+        .append(translationNamesColumnsFor("dataelement"))
+        .append(SPACED_FROM_DATA_ELEMENT)
+        .append(JOINS)
+        .append(translationNamesJoinsOn("dataelement"));
 
     return sql.toString();
   }
@@ -193,7 +216,8 @@ private String selectAllRowsIgnoringAnyTranslation() {
         .append(", dataelement.name as i18n_first_name, cast (null as text) as i18n_second_name")
         .append(
             ", dataelement.shortname as i18n_first_shortname, cast (null as text) as i18n_second_shortname")
-        .append(" from dataelement ")
+        .append(SPACED_FROM_DATA_ELEMENT)
+        .append(JOINS)
         .toString();
   }
 }
diff --git a/...-services/dhis-service-core/src/main/java/org/hisp/dhis/dataitem/query/DataItemQuery.java b/...-services/dhis-service-core/src/main/java/org/hisp/dhis/dataitem/query/DataItemQuery.java
@@ -37,6 +37,8 @@
  * @author maikel arabori
  */
 public interface DataItemQuery {
+  String CAST_NULL_AS_TEXT = "cast (null as text)";
+
   /**
    * Builds and returns the SQL statement required by the implementation.
    *

diff --git a/...s-services/dhis-service-core/src/main/java/org/hisp/dhis/dataitem/query/DataSetQuery.java b/...s-services/dhis-service-core/src/main/java/org/hisp/dhis/dataitem/query/DataSetQuery.java
@@ -27,6 +27,7 @@
  */
 package org.hisp.dhis.dataitem.query;
 
+import static java.util.stream.Collectors.joining;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.always;
 import static org.hisp.dhis.dataitem.query.shared.FilteringStatement.displayNameFiltering;
@@ -50,7 +51,9 @@
 import static org.hisp.dhis.dataitem.query.shared.UserAccessStatement.READ_ACCESS;
 import static org.hisp.dhis.dataitem.query.shared.UserAccessStatement.sharingConditions;
 
+import java.util.List;
 import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.lang3.tuple.Pair;
 import org.hisp.dhis.common.BaseIdentifiableObject;
 import org.hisp.dhis.dataitem.query.shared.OptionalFilterBuilder;
 import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
@@ -65,12 +68,23 @@
 @Component
 public class DataSetQuery implements DataItemQuery {
   private static final String COMMON_COLUMNS =
-      "cast (null as text) as program_name, cast (null as text) as program_uid,"
-          + " cast (null as text) as program_shortname, dataset.uid as item_uid, dataset.name as item_name,"
-          + " dataset.shortname as item_shortname, cast (null as text) as item_valuetype, dataset.code as item_code,"
-          + " dataset.sharing as item_sharing, cast (null as text) as item_domaintype,"
-          + " cast('REPORTING_RATE' as text) as item_type,"
-          + " cast (null as text) as expression";
+      List.of(
+              Pair.of("program_name", CAST_NULL_AS_TEXT),
+              Pair.of("program_uid", CAST_NULL_AS_TEXT),
+              Pair.of("program_shortname", CAST_NULL_AS_TEXT),
+              Pair.of("item_uid", "dataset.uid"),
+              Pair.of("item_name", "dataset.name"),
+              Pair.of("item_shortname", "dataset.shortname"),
+              Pair.of("item_valuetype", CAST_NULL_AS_TEXT),
+              Pair.of("item_code", "dataset.code"),
+              Pair.of("item_sharing", "dataset.sharing"),
+              Pair.of("item_domaintype", CAST_NULL_AS_TEXT),
+              Pair.of("item_type", "cast ('REPORTING_RATE' as text)"),
+              Pair.of("expression", CAST_NULL_AS_TEXT),
+              Pair.of("optionset_uid", CAST_NULL_AS_TEXT))
+          .stream()
+          .map(pair -> pair.getRight() + " as " + pair.getLeft())
+          .collect(joining(", "));
 
   @Override
   public String getStatement(MapSqlParameterSource paramsMap) {