feat: ddi indexing

.github/workflows/test.yaml

@@ -13,7 +13,7 @@ env:
 
 jobs:
   test:
-    if: ${{ (github.event.pull_request.draft == false) && !contains(github.event.pull_request.labels.*.name, 'publish-snapshot')
+    if: ${{ (github.event.pull_request.draft == false) && !contains(github.event.pull_request.labels.*.name, 'publish-snapshot') }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

README.md

@@ -63,6 +63,35 @@ This example can be applied to any DDI Lifecycle object: `CodeList`, `Sequence`,
 
 Useful link: [DDI model documentation](https://ddialliance.github.io/ddimodel-web/DDI-L-3.3/)
 
+## Other features
+
+### Indexing of a DDI object
+
+You can index the objects contained within a DDI object.
+
+```java
+DDIIndex ddiIndex = new DDIIndex();
+// Perform indexing
+ddiIndex.indexDDIObject(someDDIObject);
+// Get an object within the index
+AbstractIdentifiableType innerObject = ddiIndex.get("some-inner-object-id");
+// The result can be typed
+VariableType variable = ddiIndex.get("some-variable-id", VariableType.class);
+// Get the parent object in the hierarchy
+VariableSchemeType variableScheme = ddiIndex.getParent("some-variable-id", VariableScheme.class);
+```
+
+### Utilities
+
+XMLBeans API is pretty verbose, a utility class of the lib offers some QOE methods:
+
+```java
+VariableType variable = VariableType.Factory.newInstance();
+DDIUtils.setIdValue(variable, "foo-id");
+DDIUtils.getIdValue(variable) // "foo-id"
+DDIUtils.ddiToString(variable) // "VariableTypeImpl[id=foo-id]"
+```
+
 ## Requests
 
-If you have a question or bug report, feel free to open an issue.
+If you have a question, request or bug report, feel free to open an issue.

build.gradle.kts

@@ -4,7 +4,7 @@ plugins {
 
 allprojects {
     group = "fr.insee.ddi"
-    version = "1.0.0"
+    version = "1.1.0"
 }
 
 tasks.register("printVersion") {

model/.gitignore

@@ -1,4 +1,5 @@
 # Generated sources
-src/main/java/*
+src/main/java/fr/insee/ddi/lifecycle33/*
+src/main/java/org/*
 # Generated resources
-src/main/resources/org/apache/xmlbeans/*
+src/main/resources/org/apache/xmlbeans/*

model/build.gradle.kts

@@ -29,6 +29,8 @@ dependencies {
     api("org.apache.xmlbeans:xmlbeans:5.2.0")
     // This dependency is used internally, and not exposed to consumers on their own compile classpath.
     implementation("org.apache.logging.log4j:log4j-core:2.21.1")
+    //
+    implementation("org.springframework:spring-beans:6.1.11")
 
     // Use JUnit Jupiter for testing.
     testImplementation("org.junit.jupiter:junit-jupiter:5.9.3")

model/src/main/java/fr/insee/ddi/exception/DuplicateIdException.java

@@ -0,0 +1,12 @@
+package fr.insee.ddi.exception;
+
+/**
+ * Exception to be thrown if duplicate identifiers are detected in a DDI object.
+ */
+public class DuplicateIdException extends RuntimeException {
+
+    public DuplicateIdException(String message) {
+        super(message);
+    }
+
+}

model/src/main/java/fr/insee/ddi/exception/IndexingException.java

@@ -0,0 +1,16 @@
+package fr.insee.ddi.exception;
+
+/**
+ * Exception to be thrown if an unexpected exception occurs during DDI indexing.
+ */
+public class IndexingException extends RuntimeException {
+
+    public IndexingException(String message) {
+        super(message);
+    }
+
+    public IndexingException(String message, Exception e) {
+        super(message, e);
+    }
+
+}

model/src/main/java/fr/insee/ddi/index/DDIIndex.java

@@ -0,0 +1,194 @@
+package fr.insee.ddi.index;
+
+import fr.insee.ddi.exception.DuplicateIdException;
+import fr.insee.ddi.exception.IndexingException;
+import fr.insee.ddi.lifecycle33.instance.DDIInstanceDocument;
+import fr.insee.ddi.lifecycle33.reusable.AbstractIdentifiableType;
+import fr.insee.ddi.utils.DDIUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.beans.BeanWrapper;
+import org.springframework.beans.BeanWrapperImpl;
+import org.springframework.core.convert.TypeDescriptor;
+
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.InvocationTargetException;
+import java.util.*;
+
+/**
+ * Class designed to store all DDI identifiable objects within a DDI object in a flat map.
+ * Also contains a parents map that make the link between each object and its parent.
+ */
+public class DDIIndex {
+
+    private static final Logger log = LogManager.getLogger();
+
+    /** Index of DDI identifiable objects.
+     * Key: a DDI object identifier
+     * Value: the DDI object with corresponding identifier. */
+    private Map<String, AbstractIdentifiableType> index;
+
+    /** Map containing nesting relationships between objects in index.
+     * Key: a DDI object identifier
+     * Value: the identifier of its parent object */
+    private Map<String, String> parentsMap;
+
+    private void setup() {
+        index = new HashMap<>();
+        parentsMap = new HashMap<>();
+    }
+
+    /**
+     * Stores all DDI identifiable objects that are in the given DDI document in the index.
+     * @param ddiInstanceDocument A DDIInstanceDocument.
+     * @throws DuplicateIdException if two objects with the same identifier are found.
+     */
+    public void indexDDI(DDIInstanceDocument ddiInstanceDocument) throws DuplicateIdException {
+        indexDDIObject(ddiInstanceDocument.getDDIInstance());
+    }
+
+    /**
+     * Stores all DDI identifiable objects that are in the given DDI object in the index.
+     * @param ddiObject A DDI identifiable object.
+     * @throws DuplicateIdException if two objects with the same identifier are found.
+     */
+    public void indexDDIObject(AbstractIdentifiableType ddiObject) throws DuplicateIdException {
+        log.info("Indexing DDI object {}...", DDIUtils.ddiToString(ddiObject));
+        setup();
+        recursiveIndexing(ddiObject);
+        log.info("Finished indexing of DDI object.");
+    }
+
+    /**
+     * In DDI, the most generic object is the AbstractIdentifiableType
+     * (i.e. each DDI object that has an id is an AbstractIdentifiableType).
+     * This method recursively path through all AbstractIdentifiableType objects within the given object.
+     * @param ddiObject A AbstractIdentifiableType object.
+     */
+    private void recursiveIndexing(AbstractIdentifiableType ddiObject) throws IndexingException, DuplicateIdException {
+
+        // Get the DDI object id
+        String ddiObjectId = !ddiObject.getIDList().isEmpty() ? ddiObject.getIDArray(0).getStringValue() : null;
+        if (ddiObjectId == null)
+            throw new IndexingException("DDI object with null identifier encountered while indexing.");
+
+        // Put the object in the map under the id (there should never be duplicate ids in DDI documents)
+        index.merge(ddiObjectId, ddiObject, (oldDDIObject, newDDIObject) -> {
+            throw new DuplicateIdException(String.format("Duplicate ID \"%s\" found in given DDI.", ddiObjectId));
+        });
+
+        // Use Spring BeanWrapper to iterate on object property descriptors
+        BeanWrapper beanWrapper = new BeanWrapperImpl(ddiObject);
+        Iterator<PropertyDescriptor> iterator = Arrays.stream(beanWrapper.getPropertyDescriptors())
+                .filter(propertyDescriptor -> !propertyDescriptor.getName().equals("class"))
+                .iterator();
+        while (iterator.hasNext()) {
+            PropertyDescriptor propertyDescriptor = iterator.next();
+
+            // In DDI classes, everything is in a list
+            if (List.class.isAssignableFrom(propertyDescriptor.getPropertyType())) {
+
+                // Use Spring TypeDescriptor to determine the content type of the list
+                TypeDescriptor typeDescriptor = beanWrapper.getPropertyTypeDescriptor(propertyDescriptor.getName());
+                assert typeDescriptor != null;
+                Class<?> listContentType = typeDescriptor.getResolvableType().getGeneric(0).getRawClass();
+
+                // In some DDI objects, there are some methods (generated by xmlbeans) that does not interest us
+                assert listContentType != null || propertyDescriptor.getName().equals("listValue")
+                        || propertyDescriptor.getName().equals("limitArrayIndex");
+
+                // Check that the list content applies for AbstractIdentifiableType
+                if (listContentType != null && AbstractIdentifiableType.class.isAssignableFrom(listContentType)) {
+
+                    // Now that we have what we want, index list content
+                    indexListContent(ddiObject, ddiObjectId, propertyDescriptor);
+                }
+            }
+        }
+
+    }
+
+    private void indexListContent(AbstractIdentifiableType ddiObject, String ddiObjectId, PropertyDescriptor propertyDescriptor) {
+        try {
+            // Iteration on each object in the list.
+            @SuppressWarnings("unchecked") // https://stackoverflow.com/a/4388173/13425151
+            Collection<AbstractIdentifiableType> ddiCollection = (Collection<AbstractIdentifiableType>) propertyDescriptor.getReadMethod().invoke(ddiObject);
+            for (AbstractIdentifiableType ddiObject2 : ddiCollection) {
+                // Keep track of link between nested objects
+                parentsMap.put(ddiObject2.getIDArray(0).getStringValue(), ddiObjectId);
+                // Recursive call of the function
+                recursiveIndexing(ddiObject2);
+            }
+        } catch (IllegalAccessException | InvocationTargetException e) {
+            throw new IndexingException(String.format(
+                    "Error when calling read method from property descriptor '%s' in class %s.",
+                    propertyDescriptor.getName(), ddiObject.getClass()),
+                    e);
+        }
+    }
+
+    /** Returns the inner index. */
+    public Map<String, AbstractIdentifiableType> getIndex() {
+        return index;
+    }
+
+    /**
+     * Returns the DDI object corresponding to the given identifier.
+     * @param ddiObjectId String identifier value.
+     * @return The DDI object corresponding to the given identifier.
+     * @throws NoSuchElementException if there is no object under given identifier.
+     */
+    public AbstractIdentifiableType get(String ddiObjectId) {
+        AbstractIdentifiableType object = index.get(ddiObjectId);
+        if (object == null)
+            throw new NoSuchElementException(String.format("Index has no object with id '%s'.", ddiObjectId));
+        return object;
+    }
+
+    /**
+     * Returns the DDI object corresponding to the given identifier, cast in the given type.
+     * @param ddiObjectId String identifier value.
+     * @param clazz Class into which the result should be cast.
+     * @return The DDI object corresponding to the given identifier, cast in the given type.
+     * @param <T> Subtype of DDI AbstractIdentifiableType.
+     * @throws NoSuchElementException if there is no object under given identifier.
+     * @throws ClassCastException if the given object cannot be cast to the given type.
+     */
+    public <T extends AbstractIdentifiableType> T get(String ddiObjectId, Class<T> clazz) {
+        AbstractIdentifiableType object = this.get(ddiObjectId);
+        if (! clazz.isInstance(object))
+            throw new ClassCastException(String.format(
+                    "Index object with id '%s' is of type %s that cannot be cast to %s.",
+                    ddiObjectId, ddiObjectId.getClass(), clazz));
+        return clazz.cast(object);
+    }
+
+    /**
+     * Checks if the given identifier is present in the index.
+     * @param ddiObjectId String identifier value.
+     * @return True if the index contains the given identifier.
+     */
+    public boolean containsId(String ddiObjectId) {
+        return index.containsKey(ddiObjectId);
+    }
+
+    /**
+     * Returns the parent object of DDI object with given identifier.
+     * @param ddiObjectId String identifier value.
+     * @throws NoSuchElementException if the parent object for given identifier cannot be found.
+     */
+    public AbstractIdentifiableType getParent(String ddiObjectId) {
+        return this.get(parentsMap.get(ddiObjectId));
+    }
+
+    /**
+     * Returns the parent object of DDI object with given identifier.
+     * @param ddiObjectId String identifier value.
+     * @throws NoSuchElementException if the parent object for given identifier cannot be found.
+     * @throws ClassCastException if the given object cannot be cast to the given type.
+     */
+    public <T extends AbstractIdentifiableType> T getParent(String ddiObjectId, Class<T> clazz) {
+        return this.get(parentsMap.get(ddiObjectId), clazz);
+    }
+
+}

model/src/main/java/fr/insee/ddi/utils/DDIUtils.java

@@ -0,0 +1,49 @@
+package fr.insee.ddi.utils;
+
+import fr.insee.ddi.lifecycle33.reusable.AbstractIdentifiableType;
+import fr.insee.ddi.lifecycle33.reusable.IDType;
+
+/**
+ * Utility class that provide some methods for DDI objects.
+ */
+public class DDIUtils {
+
+    private DDIUtils() {}
+
+    /**
+     * Returns a better representation than the "toString" method for a DDI object.
+     * @param ddiObject A DDI object.
+     * @return String representation of the object.
+     */
+    public static String ddiToString(Object ddiObject) {
+        String className = ddiObject.getClass().getSimpleName();
+        if (! (ddiObject instanceof AbstractIdentifiableType ddiIdentifiableObject))
+            return className;
+        if (ddiIdentifiableObject.getIDList().isEmpty())
+            return className + "[id=null]";
+        return className + "[id=" + ddiIdentifiableObject.getIDArray(0).getStringValue() + "]";
+    }
+
+    /**
+     * Returns the identifier of the given DDI object.
+     * @param ddiIdentifiableObject A DDI identifiable object.
+     * @return String value of the object identifier.
+     */
+    public static String getIdValue(AbstractIdentifiableType ddiIdentifiableObject) {
+        if (ddiIdentifiableObject.getIDList().isEmpty())
+            return null;
+        return ddiIdentifiableObject.getIDArray(0).getStringValue();
+    }
+
+    /**
+     * Sets the identifier value of the given DDI object.
+     * @param ddiIdentifiableObject A DDI identifiable object.
+     * @param id String identifier value.
+     */
+    public static void setIdValue(AbstractIdentifiableType ddiIdentifiableObject, String id) {
+        if (ddiIdentifiableObject.getIDList().isEmpty())
+            ddiIdentifiableObject.getIDList().add(IDType.Factory.newInstance());
+        ddiIdentifiableObject.getIDArray(0).setStringValue(id);
+    }
+
+}