Merge branch 'main' into dependabot/maven/org.apache.maven.plugins-ma…

…ven-javadoc-plugin-3.6.0
ArDoCo · Sep 22, 2023 · 83d3ef8 · 83d3ef8
2 parents d149ab4 + cfdd51e
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diff --git a/README.md b/README.md
@@ -17,9 +17,12 @@ of _[KASTEL - Institute of Information Security and Dependability](https://kaste
 the [KIT](https://www.kit.edu).
 
 ## User Interfaces
-To be able to execute the core algorithms from this repository, you can write own user interfaces that (should) use the [ArDoCoRunner](https://github.com/ArDoCo/Core/blob/main/pipeline/pipeline-core/src/main/java/edu/kit/kastel/mcse/ardoco/core/execution/runner/ArDoCoRunner.java).
 
-We provide an example Command Line Interface (CLI) at [ArDoCo/CLI](https://github.com/ArDoCo/CLI) as well as a simple Graphical User Interface (GUI) at [ArDoCo/GUI](https://github.com/ArDoCo/GUI).
+To be able to execute the core algorithms from this repository, you can write own user interfaces that (should) use
+the [ArDoCoRunner](https://github.com/ArDoCo/Core/blob/main/pipeline/pipeline-core/src/main/java/edu/kit/kastel/mcse/ardoco/core/execution/runner/ArDoCoRunner.java).
+
+We provide an example Command Line Interface (CLI) at [ArDoCo/CLI](https://github.com/ArDoCo/CLI) as well as a simple Graphical User Interface (GUI)
+at [ArDoCo/GUI](https://github.com/ArDoCo/GUI).
 
 Future user interfaces like an enhanced GUI or a web interface are planned.
 
@@ -39,6 +42,7 @@ To test the Core, you could use case studies and benchmarks provided in ..
 ## Maven
 
 ```xml
+
 <dependencies>
 	<dependency>
 		<groupId>io.github.ardoco.core</groupId>
@@ -49,7 +53,9 @@ To test the Core, you could use case studies and benchmarks provided in ..
 ```
 
 For snapshot releases, make sure to add the following repository
+
 ```xml
+
 <repositories>
 	<repository>
 		<releases>
@@ -64,9 +70,31 @@ For snapshot releases, make sure to add the following repository
 </repositories>
 ```
 
+## Microservice for text preprocessing
+
+Text preprocessing works locally, but there is also the option to host a microservice for this.
+The benefit is that the models do not need to be loaded each time, saving some runtime (and local memory).
+
+The microservice can be found at [ArDoCo/StanfordCoreNLP-Provider-Service](https://github.com/ArDoCo/StanfordCoreNLP-Provider-Service/).
+
+The microservice is secured with credentials and the usage of the microservice needs to be activated and the URL of the microservice configured.
+These settings can be provided to the execution via environment variables.
+To do so, set the following variables:
+
+```env
+NLP_PROVIDER_SOURCE=microservice
+MICROSERVICE_URL=[microservice_url]
+SCNLP_SERVICE_USER=[your_username]
+SCNLP_SERVICE_PASSWORD=[your_password]
+```
+
+The first variable `NLP_PROVIDER_SOURCE=microservice` activates the microservice usage.
+The next three variables configure the connection, and you need to provide the configuration for your deployed microservice.
+
 ## Attribution
 
-The initial version of this project is based on the master thesis [Linking Software Architecture Documentation and Models](https://doi.org/10.5445/IR/1000126194).
+The initial version of this project is based on the master
+thesis [Linking Software Architecture Documentation and Models](https://doi.org/10.5445/IR/1000126194).
 
 ## Acknowledgements
 

diff --git a/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/text/POSTag.java b/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/text/POSTag.java
@@ -1,12 +1,16 @@
 /* Licensed under MIT 2021-2023. */
 package edu.kit.kastel.mcse.ardoco.core.api.text;
 
+import java.io.IOException;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+
 /**
  * This class represents all valid part-of-speech (pos) tags
- *
  */
 public enum POSTag {
     //@formatter:off
@@ -77,4 +81,19 @@ public boolean isVerb() {
     public boolean isNoun() {
         return getTag().startsWith("NN");
     }
+
+    @JsonValue
+    public String toValue() {
+        return getTag();
+    }
+
+    @JsonCreator
+    public static POSTag forValue(String value) throws IOException {
+        try {
+            return get(value);
+        } catch (IllegalArgumentException e) {
+            throw new IOException("Cannot deserialize PosTag");
+        }
+    }
+
 }
diff --git a/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/text/Text.java b/framework/common/src/main/java/edu/kit/kastel/mcse/ardoco/core/api/text/Text.java
@@ -24,6 +24,14 @@ default int getLength() {
      */
     ImmutableList<Word> words();
 
+    /**
+     * Returns the word at the given index
+     *
+     * @param index the index
+     * @return the word at the given index
+     */
+    Word getWord(int index);
+
     /**
      * Returns the sentences of the text, ordered by appearance.
      *

diff --git a/...java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/converter/ObjectToDtoConverter.java b/...java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/converter/ObjectToDtoConverter.java
@@ -9,10 +9,14 @@
 
 import org.eclipse.collections.api.list.ImmutableList;
 
-import edu.kit.kastel.mcse.ardoco.core.api.text.*;
+import edu.kit.kastel.mcse.ardoco.core.api.text.DependencyTag;
+import edu.kit.kastel.mcse.ardoco.core.api.text.POSTag;
+import edu.kit.kastel.mcse.ardoco.core.api.text.Phrase;
+import edu.kit.kastel.mcse.ardoco.core.api.text.Sentence;
+import edu.kit.kastel.mcse.ardoco.core.api.text.Text;
+import edu.kit.kastel.mcse.ardoco.core.api.text.Word;
 import edu.kit.kastel.mcse.ardoco.core.textproviderjson.dto.IncomingDependencyDto;
 import edu.kit.kastel.mcse.ardoco.core.textproviderjson.dto.OutgoingDependencyDto;
-import edu.kit.kastel.mcse.ardoco.core.textproviderjson.dto.PosTag;
 import edu.kit.kastel.mcse.ardoco.core.textproviderjson.dto.SentenceDto;
 import edu.kit.kastel.mcse.ardoco.core.textproviderjson.dto.TextDto;
 import edu.kit.kastel.mcse.ardoco.core.textproviderjson.dto.WordDto;
@@ -27,7 +31,7 @@ public class ObjectToDtoConverter {
 
     /**
      * converts an ArDoCo text into a text DTO
-     * 
+     *
      * @param text the ArDoCo text
      * @return the text DTO
      */
@@ -74,7 +78,7 @@ private WordDto convertToWordDTO(Word word) throws NotConvertableException {
         wordDTO.setText(word.getText());
         wordDTO.setLemma(word.getLemma());
         try {
-            wordDTO.setPosTag(PosTag.forValue(word.getPosTag().toString()));
+            wordDTO.setPosTag(POSTag.forValue(word.getPosTag().toString()));
         } catch (IOException e) {
             throw new NotConvertableException(String.format("IOException when converting word with id %d to WordDto: PosTag not found.", wordDTO.getId()));
         }

diff --git a/...vider-json/src/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/dto/PosTag.java b/...vider-json/src/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/dto/PosTag.java
diff --git a/...ider-json/src/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/dto/WordDto.java b/...ider-json/src/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/dto/WordDto.java
@@ -5,7 +5,9 @@
 import java.util.List;
 import java.util.Objects;
 
-import com.fasterxml.jackson.annotation.*;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import edu.kit.kastel.mcse.ardoco.core.api.text.POSTag;
 
 /**
  * Definition of a word
@@ -17,7 +19,7 @@ public class WordDto {
     private List<OutgoingDependencyDto> outgoingDependencies = new ArrayList<>();
     private long sentenceNo;
     private String text;
-    private PosTag posTag;
+    private POSTag posTag;
 
     /**
      * The id of the word. Should be ascending from 1 for the first word in the text.
@@ -72,12 +74,12 @@ public void setOutgoingDependencies(List<OutgoingDependencyDto> value) {
     }
 
     @JsonProperty("posTag")
-    public PosTag getPosTag() {
+    public POSTag getPosTag() {
         return posTag;
     }
 
     @JsonProperty("posTag")
-    public void setPosTag(PosTag value) {
+    public void setPosTag(POSTag value) {
         this.posTag = value;
     }
 

diff --git a/...src/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/textobject/PhraseImpl.java b/...src/main/java/edu/kit/kastel/mcse/ardoco/core/textproviderjson/textobject/PhraseImpl.java
@@ -22,24 +22,28 @@
 public class PhraseImpl implements Phrase {
     private static final String PUNCTUATION_WITH_SPACE = "\\s+([.,;:?!])";
     private static final String BRACKETS_WITH_SPACE = "\\s+([()\\[\\]{}<>])";
+    private final PhraseType type;
+    private final ImmutableList<Phrase> childPhrases;
     private final ImmutableList<Word> nonPhraseWords;
     private ImmutableList<Word> phraseWords;
-
+    private ImmutableList<Word> containedWords;
+    private ImmutableList<Phrase> subPhrases;
+    private ImmutableSortedMap<Word, Integer> phraseVector;
+    private int sentenceNo = -1;
     private String text;
 
-    private final PhraseType type;
-
-    private final List<Phrase> childPhrases;
-
     public PhraseImpl(ImmutableList<Word> nonPhraseWords, PhraseType type, List<Phrase> childPhrases) {
         this.nonPhraseWords = nonPhraseWords == null ? Lists.immutable.empty() : nonPhraseWords;
         this.type = type;
-        this.childPhrases = childPhrases;
+        this.childPhrases = Lists.immutable.ofAll(childPhrases);
     }
 
     @Override
-    public int getSentenceNo() {
-        return getContainedWords().get(0).getSentenceNo();
+    public synchronized int getSentenceNo() {
+        if (sentenceNo < 0) {
+            sentenceNo = getContainedWords().get(0).getSentenceNo();
+        }
+        return sentenceNo;
     }
 
     @Override
@@ -60,70 +64,78 @@ public PhraseType getPhraseType() {
     }
 
     @Override
-    public ImmutableList<Word> getContainedWords() {
-        if (phraseWords == null) {
-            List<Word> collectedWords = new ArrayList<>();
-            for (Phrase subphrase : childPhrases) {
-                collectedWords.addAll(subphrase.getContainedWords().castToList());
+    public synchronized ImmutableList<Word> getContainedWords() {
+        if (containedWords == null) {
+            if (phraseWords == null) {
+                List<Word> collectedWords = new ArrayList<>();
+                for (Phrase subphrase : childPhrases) {
+                    collectedWords.addAll(subphrase.getContainedWords().castToList());
+                }
+                this.phraseWords = Lists.immutable.ofAll(collectedWords);
             }
-            this.phraseWords = Lists.immutable.ofAll(collectedWords);
+
+            MutableList<Word> words = Lists.mutable.ofAll(nonPhraseWords);
+            words.addAllIterable(phraseWords);
+            words.sortThis(Comparator.comparingInt(Word::getPosition));
+            containedWords = words.toImmutable();
         }
 
-        MutableList<Word> words = Lists.mutable.ofAll(nonPhraseWords);
-        words.addAllIterable(phraseWords);
-        words.sortThis(Comparator.comparingInt(Word::getPosition));
-        return words.toImmutable();
+        return containedWords;
     }
 
     @Override
-    public ImmutableList<Phrase> getSubPhrases() {
-        List<Phrase> subPhrases = new ArrayList<>(childPhrases);
-        for (Phrase childPhrase : childPhrases) {
-            subPhrases.addAll(childPhrase.getSubPhrases().toList());
+    public synchronized ImmutableList<Phrase> getSubPhrases() {
+        if (subPhrases == null) {
+            MutableList<Phrase> tempSubPhrases = Lists.mutable.ofAll(childPhrases);
+            for (Phrase childPhrase : childPhrases) {
+                tempSubPhrases.addAll(childPhrase.getSubPhrases().toList());
+            }
+            subPhrases = tempSubPhrases.toImmutable();
         }
-        return Lists.immutable.ofAll(subPhrases);
+        return subPhrases;
     }
 
     @Override
     public boolean isSuperPhraseOf(Phrase other) {
-        List<Phrase> subphrases = this.childPhrases;
+        MutableList<Phrase> subphrases = Lists.mutable.ofAll(this.getSubPhrases());
         while (!subphrases.isEmpty()) {
             if (subphrases.contains(other)) {
                 return true;
             }
-            List<Phrase> newSubphrases = new ArrayList<>();
-            for (Phrase subphrase : subphrases) {
-                newSubphrases.addAll(subphrase.getSubPhrases().castToList());
-            }
-            subphrases = newSubphrases;
+            subphrases = getSubPhrasesOfPhrases(subphrases);
         }
         return false;
     }
 
+    private static MutableList<Phrase> getSubPhrasesOfPhrases(MutableList<Phrase> subphrases) {
+        MutableList<Phrase> subPhrasesOfPhrases = Lists.mutable.empty();
+        for (Phrase subphrase : subphrases) {
+            subPhrasesOfPhrases.addAll(subphrase.getSubPhrases().castToList());
+        }
+        return subPhrasesOfPhrases;
+    }
+
     @Override
     public boolean isSubPhraseOf(Phrase other) {
-        List<Phrase> subphrases = other.getSubPhrases().castToList();
+        MutableList<Phrase> subphrases = Lists.mutable.ofAll(other.getSubPhrases());
         while (!subphrases.isEmpty()) {
             if (subphrases.contains(this)) {
                 return true;
             }
-            List<Phrase> newSubphrases = new ArrayList<>();
-            for (Phrase subphrase : subphrases) {
-                newSubphrases.addAll(subphrase.getSubPhrases().castToList());
-            }
-            subphrases = newSubphrases;
+            subphrases = getSubPhrasesOfPhrases(subphrases);
         }
         return false;
     }
 
     @Override
-    public ImmutableSortedMap<Word, Integer> getPhraseVector() {
-        MutableSortedMap<Word, Integer> phraseVector = SortedMaps.mutable.empty();
-
-        var grouped = getContainedWords().groupBy(Word::getText).toMap();
-        grouped.forEach((key, value) -> phraseVector.put(value.getAny(), value.size()));
-
-        return phraseVector.toImmutable();
+    public synchronized ImmutableSortedMap<Word, Integer> getPhraseVector() {
+        if (this.phraseVector == null) {
+            MutableSortedMap<Word, Integer> tempPhraseVector = SortedMaps.mutable.empty();
+            var grouped = getContainedWords().groupBy(Word::getText).toMap();
+            grouped.forEach((key, value) -> tempPhraseVector.put(value.getAny(), value.size()));
+            this.phraseVector = tempPhraseVector.toImmutable();
+        }
+        return this.phraseVector;
     }
 
     @Override