Add informal diagram consistency pipeline steps (#308)

* Adapt code model to support nested classes

* Extend code model to store references of types to other types

* Move code from thesis repo into ArDoCo core

* Fix some test

* Merge the two existing diagram classes

* Fix the large graph test

* Fix version name

* Update stages/diagram-consistency/pom.xml

Co-authored-by: Dominik Fuchß <develop@fuchss.org>

* Adapt pom.xml files as reviewed and adapt to changes related to package structure

* Update framework/common/pom.xml

* Apply spotless

* Reset benchmark

* Squashed 'tests/tests-base/src/main/resources/benchmark/' changes from 7675243a..daeaee7e

daeaee7e Update code models to contain parent class and reference info (#12)
4fae195e Format Code Model. Fix #13
814aa945 Remove duplicate in GS

git-subtree-dir: tests/tests-base/src/main/resources/benchmark
git-subtree-split: daeaee7e6273722b44a1a82b5d7bdd204edd743c

* Let evaluation code extract code models if no already extracted model available

* Apply spotless

* Use assertion messages to gain more information about the occurring failures

* When extracting a code model, clone first

* Delete directory before cloning

* Squashed 'tests/tests-base/src/main/resources/benchmark/' changes from daeaee7e..9bbc3a89

9bbc3a89 Update code models to contain parent class and reference info, using new formatting (#16)
fe5a8549 Update the codemodel to be more (human) readable

git-subtree-dir: tests/tests-base/src/main/resources/benchmark
git-subtree-split: 9bbc3a89677ffba98bb861f0c0206a93c61ec5d1

* Work on code smells

* Remove annotation that leads to compile error

* Register diagram-consistency to report

* Fix loading of ACM

* Remove commented out import

---------

Co-authored-by: Dominik Fuchß <dominik.fuchss@kit.edu>

framework/common/pom.xml

@@ -45,6 +45,11 @@
       <groupId>org.eclipse.jgit</groupId>
       <artifactId>org.eclipse.jgit</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.jgrapht</groupId>
+      <artifactId>jgrapht-core</artifactId>
+      <version>${jgrapht.version}</version>
+    </dependency>
     <dependency>
       <groupId>org.junit.jupiter</groupId>
       <artifactId>junit-jupiter-engine</artifactId>

framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/DiagramMatchingModelSelectionState.java

@@ -0,0 +1,123 @@
+/* Licensed under MIT 2023. */
+package edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency.common.ElementRole;
+import edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency.common.WeightedTextSimilarity;
+import edu.kit.kastel.mcse.ardoco.core.api.models.ModelType;
+import edu.kit.kastel.mcse.ardoco.core.architecture.Deterministic;
+import edu.kit.kastel.mcse.ardoco.core.data.PipelineStepData;
+
+/**
+ * Stores data created during the model selection process, as well as the selection itself. The data includes a created
+ * text similarity function and all occurrences of diagram elements in models.
+ */
+@Deterministic
+public interface DiagramMatchingModelSelectionState extends PipelineStepData {
+    /**
+     * The ID of this state.
+     */
+    String ID = "DiagramMatchingModelSelectionState";
+
+    /**
+     * Gets the model types that are in principle available, meaning their loading is attempted.
+     *
+     * @return The model types.
+     */
+    Set<ModelType> getAvailableModelTypes();
+
+    /**
+     * Sets the model types that are in principle available, meaning their loading is attempted.
+     *
+     * @param availableModelTypes
+     *                            The model types.
+     */
+    void setAvailableModelTypes(Set<ModelType> availableModelTypes);
+
+    /**
+     * Gets the similarity function.
+     *
+     * @return The similarity function.
+     */
+    WeightedTextSimilarity getSimilarityFunction();
+
+    /**
+     * Sets the similarity function.
+     *
+     * @param similarity
+     *                   The similarity function.
+     */
+    void setSimilarityFunction(WeightedTextSimilarity similarity);
+
+    /**
+     * Gets the model type that is selected to be matched with the diagram.
+     *
+     * @return The model type.
+     */
+    Set<ModelType> getSelection();
+
+    /**
+     * Sets the models that are selected to be matched with the diagram.
+     *
+     * @param modelTypes
+     *                   The model types.
+     */
+    void setSelection(Set<ModelType> modelTypes);
+
+    /**
+     * Adds an occurrence of a diagram element in a model.
+     *
+     * @param diagramID The ID of the diagram element.
+     * @param modelType The model the model element is in.
+     * @param modelID   The ID of the model element.
+     * @param role      The role of the model element.
+     */
+    void addOccurrence(String diagramID, ModelType modelType, String modelID, ElementRole role);
+
+    /**
+     * Get all occurrences of a diagram element in a model.
+     *
+     * @param diagramID The ID of the diagram element.
+     * @param modelType The model to get the occurrences in.
+     * @return The occurrences.
+     */
+    List<Occurrence> getOccurrences(String diagramID, ModelType modelType);
+
+    /**
+     * Get all occurrences of a diagram element in all models.
+     *
+     * @param diagramID
+     *                  The ID of the diagram element.
+     * @return The occurrences.
+     */
+    List<Occurrence> getOccurrences(String diagramID);
+
+    /**
+     * Gets the explanation why the model type was selected.
+     *
+     * @return The explanation, which is a match value for each model type.
+     */
+    Map<ModelType, Double> getSelectionExplanation();
+
+    /**
+     * Sets the explanation why the model type was selected.
+     *
+     * @param explanation
+     *                    The explanation, which is a match value for each model type.
+     */
+    void setSelectionExplanation(Map<ModelType, Double> explanation);
+
+    /**
+     * Describes an occurrence of a diagram element in a model.
+     *
+     * @param modelID
+     *                The ID of the model element.
+     * @param role
+     *                The role of the model element.
+     */
+    public record Occurrence(String modelID, ElementRole role) {
+    }
+}

framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/DiagramModelInconsistencyState.java

@@ -0,0 +1,56 @@
+/* Licensed under MIT 2023. */
+package edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency;
+
+import java.util.List;
+
+import edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency.common.inconsistencies.Inconsistency;
+import edu.kit.kastel.mcse.ardoco.core.api.models.ModelType;
+import edu.kit.kastel.mcse.ardoco.core.data.PipelineStepData;
+
+/**
+ * Contains information about found inconsistencies between the diagram and the given models.
+ */
+public interface DiagramModelInconsistencyState extends PipelineStepData {
+    /**
+     * The ID of this state.
+     */
+    String ID = "DiagramModelInconsistencyState";
+
+    /**
+     * Adds an inconsistency.
+     *
+     * @param modelType     The model type to add the inconsistency for.
+     * @param inconsistency
+     *                      The inconsistency to add.
+     */
+    void addInconsistency(ModelType modelType, Inconsistency<String, String> inconsistency);
+
+    /**
+     * Returns all found inconsistencies.
+     *
+     * @param modelType The model type to get inconsistencies for.
+     * @return All inconsistencies.
+     */
+    List<Inconsistency<String, String>> getInconsistencies(ModelType modelType);
+
+    /**
+     * Set the extended inconsistencies. The extended inconsistency list is based on the basic inconsistency list but a
+     * larger selection of more concrete inconsistency types can be used.
+     *
+     * @param modelType
+     *                        The model type to set the inconsistencies for.
+     * @param inconsistencies
+     *                        The inconsistencies to set.
+     */
+    void setExtendedInconsistencies(ModelType modelType, List<Inconsistency<String, String>> inconsistencies);
+
+    /**
+     * Returns the extended inconsistencies. If no extended inconsistencies are set, the basic inconsistencies are
+     * returned.
+     *
+     * @param modelType
+     *                  The model type to get the inconsistencies for.
+     * @return The extended inconsistencies.
+     */
+    List<Inconsistency<String, String>> getExtendedInconsistencies(ModelType modelType);
+}

framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/DiagramModelLinkState.java

@@ -0,0 +1,38 @@
+/* Licensed under MIT 2023. */
+package edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency;
+
+import org.eclipse.collections.api.bimap.MutableBiMap;
+
+import edu.kit.kastel.mcse.ardoco.core.api.models.ModelType;
+import edu.kit.kastel.mcse.ardoco.core.data.PipelineStepData;
+
+/**
+ * Stores all results of the matching process.
+ */
+public interface DiagramModelLinkState extends PipelineStepData {
+    /**
+     * The ID of this state.
+     */
+    String ID = "DiagramModelLinkState";
+
+    /**
+     * Adds a link between a diagram element and a model element.
+     *
+     * @param modelType
+     *                  The model type of the model in which the model element is located.
+     * @param diagramID
+     *                  The ID of the diagram element.
+     * @param modelID
+     *                  The ID of the model element.
+     */
+    void addLink(ModelType modelType, String diagramID, String modelID);
+
+    /**
+     * Get all currently stored links between the diagram and a model.
+     *
+     * @param modelType
+     *                  The type of the model.
+     * @return The links.
+     */
+    MutableBiMap<String, String> getLinks(ModelType modelType);
+}

framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/DiagramState.java

@@ -0,0 +1,30 @@
+/* Licensed under MIT 2023. */
+package edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency;
+
+import edu.kit.kastel.mcse.ardoco.core.api.diagramrecognition.Diagram;
+import edu.kit.kastel.mcse.ardoco.core.data.PipelineStepData;
+
+/**
+ * Contains the loaded diagram.
+ */
+public interface DiagramState extends PipelineStepData {
+    /**
+     * The ID in the data repository.
+     */
+    String ID = "DiagramStateData";
+
+    /**
+     * Returns the diagram.
+     *
+     * @return The diagram. May be null.
+     */
+    Diagram getDiagram();
+
+    /**
+     * Sets the diagram. Overwrites the old diagram.
+     *
+     * @param diagram
+     *                The diagram.
+     */
+    void setDiagram(Diagram diagram);
+}

framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/common/DiagramUtility.java

@@ -0,0 +1,127 @@
+/* Licensed under MIT 2023. */
+package edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency.common;
+
+import java.util.List;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.UUID;
+import java.util.stream.Collectors;
+
+import edu.kit.kastel.mcse.ardoco.core.api.diagramrecognition.Box;
+import edu.kit.kastel.mcse.ardoco.core.api.diagramrecognition.Connector;
+import edu.kit.kastel.mcse.ardoco.core.api.diagramrecognition.Diagram;
+import edu.kit.kastel.mcse.ardoco.core.api.diagramrecognition.TextBox;
+import edu.kit.kastel.mcse.ardoco.core.architecture.Deterministic;
+
+/**
+ * This class contains utility methods to use with the diagram interface.
+ */
+@Deterministic
+public class DiagramUtility {
+    private DiagramUtility() {
+    }
+
+    /**
+     * Checks if there is a connection between the two boxes.
+     * 
+     * @param diagram The diagram in which the boxes are located.
+     * @param source  The source box.
+     * @param target  The target box.
+     * @return True if there is a connection between the two boxes, false otherwise.
+     */
+    public static boolean hasConnectionBetween(Diagram diagram, Box source, Box target) {
+        return diagram.getConnectors().stream().anyMatch(connector -> isConnectionBetween(connector, source, target));
+    }
+
+    /**
+     * Checks if the connector connects the two boxes.
+     * 
+     * @param connector The connector to check.
+     * @param source    The source box.
+     * @param target    The target box.
+     * @return True if the connector connects the two boxes, false otherwise.
+     */
+    public static boolean isConnectionBetween(Connector connector, Box source, Box target) {
+        List<String> connectedBoxes = connector.getConnectedBoxes();
+        return connectedBoxes.get(0).equals(source.getUUID()) && connectedBoxes.contains(target.getUUID());
+    }
+
+    /**
+     * Returns all connectors that are outgoing from the box.
+     * 
+     * @param diagram The diagram in which the box is located.
+     * @param box     The box.
+     * @return All connectors that are outgoing from the box.
+     */
+    public static List<Connector> getOutgoingConnectors(Diagram diagram, Box box) {
+        return diagram.getConnectors().stream().filter(connector -> connector.getConnectedBoxes().get(0).equals(box.getUUID())).toList();
+    }
+
+    /**
+     * Get a map of all boxes in the diagram.
+     * 
+     * @param diagram The diagram.
+     * @return A map from the UUID of the box to the box.
+     */
+    public static SortedMap<String, Box> getBoxes(Diagram diagram) {
+        return diagram.getBoxes().stream().collect(Collectors.toMap(Box::getUUID, box -> box, (a, b) -> b, TreeMap::new));
+    }
+
+    /**
+     * Get the targets of the connector.
+     *
+     * @param connector The connector.
+     * @param boxes     A UUID-box map.
+     * @return The targets of the connector.
+     */
+    public static List<Box> getTargets(Connector connector, SortedMap<String, Box> boxes) {
+        return connector.getConnectedBoxes().stream().skip(1).map(boxes::get).toList();
+    }
+
+    /**
+     * Get the text of the box.
+     * 
+     * @param box The box.
+     * @return The text of the box.
+     */
+    public static String getBoxText(Box box) {
+        return box.getTexts().stream().map(TextBox::getText).collect(Collectors.joining(" "));
+    }
+
+    /**
+     * Get the contained boxes of the box.
+     * 
+     * @param box   The box.
+     * @param boxes A UUID-box map.
+     * @return The contained boxes of the box.
+     */
+    public static List<Box> getContainedBoxes(Box box, SortedMap<String, Box> boxes) {
+        return box.getContainedBoxes().stream().map(boxes::get).toList();
+    }
+
+    /**
+     * Add a box to the diagram.
+     * 
+     * @param diagram The diagram.
+     * @param text    The text of the box.
+     * @return The added box.
+     */
+    public static Box addBox(Diagram diagram, String text) {
+        TextBox textBox = new TextBox(0, 0, 0, 0, 1.0, text, null);
+        Box box = new Box(String.valueOf(diagram.getBoxes().size()), new int[] { 0, 0, 0, 0 }, 1.0, null, List.of(textBox), null);
+
+        diagram.addBox(box);
+        return box;
+    }
+
+    /**
+     * Add a connector between the two boxes.
+     * 
+     * @param diagram The diagram in which the boxes are located.
+     * @param source  The source box.
+     * @param target  The target box.
+     */
+    public static void addConnector(Diagram diagram, Box source, Box target) {
+        diagram.addConnector(new Connector(UUID.randomUUID().toString(), List.of(source.getUUID(), target.getUUID()), List.of()));
+    }
+}