Try to merge (still wip)

ArDoCo · Jan 12, 2024 · 1c849ec · 1c849ec
1 parent d576147
commit 1c849ec
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Showing 33 changed files with 236 additions and 168 deletions.
diff --git a/...in/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/common/DiagramUtility.java b/...in/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/common/DiagramUtility.java
@@ -1,4 +1,4 @@
-/* Licensed under MIT 2023. */
+/* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.api.diagramconsistency.common;
 
 import java.util.List;
@@ -108,7 +108,7 @@ public static List<Box> getContainedBoxes(Box box, SortedMap<String, Box> boxes)
      */
     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);
+        Box box = new Box(diagram, String.valueOf(diagram.getBoxes().size()), new int[] { 0, 0, 0, 0 }, 1.0, null, List.of(textBox), null);
 
         diagram.addBox(box);
         return box;

diff --git a/.../main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/common/JsonMapping.java b/.../main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramconsistency/common/JsonMapping.java
diff --git a/...work/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/Box.java b/...work/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/diagramrecognition/Box.java
@@ -32,11 +32,12 @@ public class Box extends DiagramElement implements Serializable {
     private List<TextBox> textBoxes = new ArrayList<>();
     @JsonProperty("contained")
     private List<String> containedBoxes = new ArrayList<>();
-    private transient Color dominatingColor = null;
+    @JsonProperty("dominatingColor")
+    private Color dominatingColor = null;
     @JsonIgnore
     private SortedSet<String> references = new TreeSet<>();
 
-    private static String calculateUUID(int[] coordinates) {
+    protected static String calculateUUID(int[] coordinates) {
         return String.format("Box [%s]", getBoundingBoxConcat(coordinates));
     }
 
@@ -49,6 +50,26 @@ public static String getBoundingBoxConcat(int[] coordinates) {
         return Arrays.stream(coordinates).mapToObj((Integer::toString)).reduce((l, r) -> l + "-" + r).orElseThrow();
     }
 
+    /**
+     * Create a new box that is detected on the image.
+     *
+     * @param diagram         the diagram the box belongs to
+     * @param uuid            the unique identifier of the box
+     * @param coordinates     the coordinates of two corners of the box in pixel. (x1,y1,x2,y2)
+     * @param confidence      a confidence value
+     * @param classification  the classification (e.g., "LABEL"), see {@link Classification} for further details
+     * @param textBoxes       the text boxes that are attached to this box
+     * @param dominatingColor a dominating color in the box (iff present)
+     */
+    public Box(Diagram diagram, String uuid, int[] coordinates, double confidence, String classification, List<TextBox> textBoxes, Color dominatingColor) {
+        super(diagram, uuid);
+        this.coordinates = coordinates;
+        this.confidence = confidence;
+        this.classification = classification;
+        this.textBoxes = textBoxes;
+        this.dominatingColor = dominatingColor;
+    }
+
     /**
      * Create a new box that is detected on the image.
      *
@@ -71,18 +92,22 @@ public Box(Diagram diagram, int[] coordinates, double confidence, String classif
     /**
      * Create a new box that is detected on the image.
      *
-     * @param diagram        the diagram this box belongs to
-     * @param coordinates    the coordinates of two corners of the box in pixel. (x1,y1,x2,y2)
-     * @param confidence     a confidence value
-     * @param classification the classification (e.g., "LABEL"), see {@link Classification} for further details
+     * @param diagram         the diagram this box belongs to
+     * @param uuid            the unique identifier of the box
+     * @param coordinates     the coordinates of two corners of the box in pixel. (x1,y1,x2,y2)
+     * @param confidence      a confidence value
+     * @param classification  the classification (e.g., "LABEL"), see {@link Classification} for further details
+     * @param dominatingColor a dominating color in the box (iff present)
      */
     @JsonCreator
-    public Box(@JacksonInject Diagram diagram, @JsonProperty("box") int[] coordinates, @JsonProperty("confidence") double confidence,
-            @JsonProperty("class") String classification) {
-        super(diagram, calculateUUID(coordinates));
+    public Box(@JacksonInject Diagram diagram, @JsonProperty("uuid") String uuid, @JsonProperty("box") int[] coordinates,
+            @JsonProperty("confidence") double confidence, @JsonProperty("class") String classification,
+            @JsonProperty("dominatingColor") Color dominatingColor) {
+        super(diagram, uuid == null ? calculateUUID(coordinates) : uuid);
         this.coordinates = coordinates;
         this.confidence = confidence;
         this.classification = classification;
+        this.dominatingColor = dominatingColor;
     }
 
     /**

diff --git a/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/JsonHandling.java b/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/JsonHandling.java
@@ -0,0 +1,26 @@
+/* Licensed under MIT 2024. */
+package edu.kit.kastel.mcse.ardoco.core.common;
+
+import com.fasterxml.jackson.annotation.JsonAutoDetect;
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+
+public final class JsonHandling {
+    private JsonHandling() {
+        throw new IllegalAccessError("Utility class");
+    }
+
+    public static ObjectMapper createObjectMapper() {
+        var objectMapper = new ObjectMapper();
+        objectMapper.configure(SerializationFeature.INDENT_OUTPUT, false);
+        objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+        objectMapper.setVisibility(objectMapper.getSerializationConfig()
+                .getDefaultVisibilityChecker() //
+                .withFieldVisibility(JsonAutoDetect.Visibility.ANY) //
+                .withGetterVisibility(JsonAutoDetect.Visibility.NONE) //
+                .withSetterVisibility(JsonAutoDetect.Visibility.NONE) //
+                .withIsGetterVisibility(JsonAutoDetect.Visibility.NONE));
+        return objectMapper;
+    }
+}
diff --git a/...in/java/edu/kit/kastel/mcse/ardoco/core/common/util/AbbreviationDisambiguationHelper.java b/...in/java/edu/kit/kastel/mcse/ardoco/core/common/util/AbbreviationDisambiguationHelper.java
@@ -1,6 +1,8 @@
 /* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.common.util;
 
+import static edu.kit.kastel.mcse.ardoco.core.common.JsonHandling.createObjectMapper;
+
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.*;
@@ -13,8 +15,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 import edu.kit.kastel.mcse.ardoco.core.api.Disambiguation;
 
 /**
@@ -212,7 +212,7 @@ static SortedSet<String> crawlAcronymFinderCom(String abbreviation) {
     protected SortedMap<String, Disambiguation> read() throws CacheException {
         try {
             logger.info("Reading abbreviations file");
-            var read = toMap(new ObjectMapper().readValue(getFile(), Disambiguation[].class));
+            var read = toMap(createObjectMapper().readValue(getFile(), Disambiguation[].class));
             logger.info("Found {} cached abbreviation", read.size());
             return read;
         } catch (IOException e) {
@@ -230,7 +230,7 @@ protected void write(SortedMap<String, Disambiguation> content) {
         Collection<Disambiguation> values = content.values();
         try (PrintWriter out = new PrintWriter(getFile())) {
             //Parse before writing to the file, so we don't mess up the entire file due to a parsing error
-            String json = new ObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(values);
+            String json = createObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(values);
             out.print(json);
             logger.info("Saved abbreviations file");
         } catch (IOException e) {

diff --git a/...ework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/util/DbPediaHelper.java b/...ework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/util/DbPediaHelper.java
@@ -1,6 +1,8 @@
 /* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.common.util;
 
+import static edu.kit.kastel.mcse.ardoco.core.common.JsonHandling.createObjectMapper;
+
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.List;
@@ -13,7 +15,6 @@
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
 
 /**
  * This class provides lists of computer- and software-related terminology. It retrieves the terminology from the DBPedia ontology using SPARQL queries. The
@@ -151,7 +152,7 @@ private List<String> runQuery(ParameterizedSparqlString query) {
     protected void write(DbPediaData r) {
         try (PrintWriter out = new PrintWriter(getFile())) {
             //Parse before writing to the file, so we don't mess up the entire file due to a parsing error
-            String json = new ObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(r);
+            String json = createObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(r);
             out.print(json);
             logger.info("Saved {} file", getIdentifier());
         } catch (IOException e) {
@@ -168,7 +169,7 @@ protected DbPediaData getDefault() {
     protected DbPediaData read() throws CacheException {
         try {
             logger.info("Reading {} file", getIdentifier());
-            return new ObjectMapper().readValue(getFile(), new TypeReference<>() {
+            return createObjectMapper().readValue(getFile(), new TypeReference<>() {
             });
         } catch (IOException e) {
             logger.error("Error reading {} file", getIdentifier());

diff --git a/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/data/PipelineStepData.java b/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/data/PipelineStepData.java
@@ -1,4 +1,4 @@
-/* Licensed under MIT 2022-2023. */
+/* Licensed under MIT 2022-2024. */
 package edu.kit.kastel.mcse.ardoco.core.data;
 
 import java.io.Serializable;
@@ -7,10 +7,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.annotation.JsonAutoDetect;
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
+import edu.kit.kastel.mcse.ardoco.core.common.JsonHandling;
 
 /**
  * This abstract class defines data that is used for the pipeline steps.
@@ -36,7 +33,7 @@ default <T extends PipelineStepData> Optional<T> asPipelineStepData(Class<T> cla
     }
 
     default String serialize() {
-        var oom = createObjectMapper();
+        var oom = JsonHandling.createObjectMapper();
         try {
             return oom.writeValueAsString(this);
         } catch (Exception e) {
@@ -46,25 +43,12 @@ default String serialize() {
     }
 
     default PipelineStepData deserialize(String data) {
-        var oom = createObjectMapper();
+        var oom = JsonHandling.createObjectMapper();
         try {
             return oom.readValue(data, this.getClass());
         } catch (Exception e) {
             logger.error(e.getMessage(), e);
             return null;
         }
     }
-
-    private static ObjectMapper createObjectMapper() {
-        var objectMapper = new ObjectMapper();
-        objectMapper.configure(SerializationFeature.INDENT_OUTPUT, false);
-        objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-        objectMapper.setVisibility(objectMapper.getSerializationConfig()
-                .getDefaultVisibilityChecker() //
-                .withFieldVisibility(JsonAutoDetect.Visibility.ANY) //
-                .withGetterVisibility(JsonAutoDetect.Visibility.NONE) //
-                .withSetterVisibility(JsonAutoDetect.Visibility.NONE) //
-                .withIsGetterVisibility(JsonAutoDetect.Visibility.NONE));
-        return objectMapper;
-    }
 }
diff --git a/...ava/edu/kit/kastel/mcse/ardoco/core/common/util/AbbreviationDisambiguationHelperTest.java b/...ava/edu/kit/kastel/mcse/ardoco/core/common/util/AbbreviationDisambiguationHelperTest.java
@@ -1,14 +1,14 @@
 /* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.common.util;
 
+import static edu.kit.kastel.mcse.ardoco.core.common.JsonHandling.createObjectMapper;
 import static org.junit.jupiter.api.Assertions.*;
 
 import java.util.List;
 
 import org.junit.jupiter.api.Test;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 
 import edu.kit.kastel.mcse.ardoco.core.api.Disambiguation;
 
@@ -31,7 +31,7 @@ void get() {
 
     @Test
     void deserialize() throws JsonProcessingException {
-        var abbr = new ObjectMapper().readValue(dbJSON, Disambiguation.class);
+        var abbr = createObjectMapper().readValue(dbJSON, Disambiguation.class);
         assertEquals("DB", abbr.getAbbreviation());
         assertTrue(abbr.getMeanings().containsAll(List.of("Database", "Decibel")));
         assertEquals(2, abbr.getMeanings().size());

diff --git a/...c/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/converter/JsonConverter.java b/...c/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/converter/JsonConverter.java
@@ -1,6 +1,8 @@
-/* Licensed under MIT 2023. */
+/* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.textproviderjson.converter;
 
+import static edu.kit.kastel.mcse.ardoco.core.common.JsonHandling.createObjectMapper;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
@@ -40,7 +42,7 @@ private JsonConverter() {
      * @return whether the json string matches the text schema
      */
     public static boolean validateJson(String json) throws IOException {
-        ObjectMapper mapper = new ObjectMapper();
+        ObjectMapper mapper = createObjectMapper();
         JsonSchemaFactory schemaFactory = JsonSchemaFactory.getInstance(SpecVersion.VersionFlag.V4);
 
         InputStream inputSchema = JsonConverter.class.getClassLoader().getResourceAsStream(SCHEMA_PATH);
@@ -69,7 +71,7 @@ public static TextDto fromJsonString(String json) throws IOException, InvalidJso
         if (!validateJson(json)) {
             throw new InvalidJsonException("The json string is no valid text DTO.");
         }
-        ObjectMapper objectMapper = new ObjectMapper();
+        ObjectMapper objectMapper = createObjectMapper();
         return objectMapper.readValue(json, TextDto.class);
     }
 
@@ -80,7 +82,7 @@ public static TextDto fromJsonString(String json) throws IOException, InvalidJso
      * @return the JSON string or null
      */
     public static String toJsonString(TextDto obj) throws IOException, InvalidJsonException {
-        ObjectMapper objectMapper = new ObjectMapper();
+        ObjectMapper objectMapper = createObjectMapper();
         String jsonString = objectMapper.writeValueAsString(obj);
         if (!validateJson(jsonString)) {
             throw new InvalidJsonException("The text DTO could not be converted into a json string. No valid text Dto");

diff --git a/.../pipeline-core/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/util/FilePrinter.java b/.../pipeline-core/src/main/java/edu/kit/kastel/mcse/ardoco/core/common/util/FilePrinter.java
@@ -1,4 +1,4 @@
-/* Licensed under MIT 2021-2023. */
+/* Licensed under MIT 2021-2024. */
 package edu.kit.kastel.mcse.ardoco.core.common.util;
 
 import static edu.kit.kastel.mcse.ardoco.core.common.util.DataRepositoryHelper.getConnectionStates;
@@ -392,6 +392,7 @@ public static void writeToFile(String filename, String text) {
      * @param text the text to write
      */
     public static void writeToFile(Path file, String text) {
+        file.getParent().toFile().mkdirs();
         try (BufferedWriter writer = Files.newBufferedWriter(file, UTF_8)) {
             writer.write(text);
         } catch (IOException e) {

diff --git a/.../src/main/java/edu/kit/kastel/mcse/ardoco/core/diagramconsistency/DiagramConsistency.java b/.../src/main/java/edu/kit/kastel/mcse/ardoco/core/diagramconsistency/DiagramConsistency.java
@@ -1,4 +1,4 @@
-/* Licensed under MIT 2023. */
+/* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.diagramconsistency;
 
 import java.io.File;
@@ -19,7 +19,7 @@
 import edu.kit.kastel.mcse.ardoco.core.diagramconsistency.agents.DiagramProviderAgent;
 import edu.kit.kastel.mcse.ardoco.core.execution.ArDoCo;
 import edu.kit.kastel.mcse.ardoco.core.execution.runner.ArDoCoRunner;
-import edu.kit.kastel.mcse.ardoco.core.models.ArCoTLModelProviderAgent;
+import edu.kit.kastel.mcse.ardoco.core.models.agents.ArCoTLModelProviderAgent;
 
 /**
  * A runner that checks the consistency of a diagram and the represented architecture/code model.

diff --git a/...se/ardoco/core/diagramconsistency/informants/DiagramElementOccurrenceFinderInformant.java b/...se/ardoco/core/diagramconsistency/informants/DiagramElementOccurrenceFinderInformant.java
@@ -1,4 +1,4 @@
-/* Licensed under MIT 2023. */
+/* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.diagramconsistency.informants;
 
 import java.util.Set;
@@ -72,7 +72,7 @@ public DiagramElementOccurrenceFinderInformant(DataRepository dataRepository) {
     }
 
     @Override
-    public void run() {
+    public void process() {
         if (this.skip) {
             return;
         }

diff --git a/...el/mcse/ardoco/core/diagramconsistency/informants/DiagramModelInconsistencyInformant.java b/...el/mcse/ardoco/core/diagramconsistency/informants/DiagramModelInconsistencyInformant.java
@@ -1,4 +1,4 @@
-/* Licensed under MIT 2023. */
+/* Licensed under MIT 2023-2024. */
 package edu.kit.kastel.mcse.ardoco.core.diagramconsistency.informants;
 
 import java.util.ArrayList;
@@ -107,7 +107,7 @@ private static void checkRulesForLooseEntities(Map<String, Entity> entities, Con
     }
 
     @Override
-    public void run() {
+    public void process() {
         DataRepository data = this.getDataRepository();
 
         ModelStates models = data.getData(ModelStates.ID, ModelStates.class).orElse(null);