Merge pull request #267 from kbss-cvut/development

[3.1.0] Release
kbss-cvut · Jul 8, 2024 · f95660a · f95660a
2 parents 6be4c40 + 687f740
commit f95660a
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diff --git a/.github/workflows/push-to-protected.yml b/.github/workflows/push-to-protected.yml
@@ -20,8 +20,8 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
-    - uses: actions/setup-java@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-java@v4
       with:
         java-version: '17'
         distribution: 'adopt'

diff --git a/.gitignore b/.gitignore
@@ -6,4 +6,4 @@ catalog-v001.xml
 **/bundle.js
 **/generated-sources
 **/java-generated
-**/npm-debug.log
+termit-doc.md
diff --git a/pom.xml b/pom.xml
@@ -7,11 +7,11 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>3.2.3</version>
+        <version>3.2.5</version>
     </parent>
 
     <artifactId>termit</artifactId>
-    <version>3.0.4</version>
+    <version>3.1.0</version>
     <name>TermIt</name>
     <description>Terminology manager based on Semantic Web technologies.</description>
     <packaging>${packaging}</packaging>
@@ -20,39 +20,19 @@
         <repository>
             <id>kbss</id>
             <url>https://kbss.felk.cvut.cz/m2repo</url>
-        </repository>
-        <repository>
-            <id>central-snapshots</id>
-            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
             <snapshots>
                 <enabled>true</enabled>
             </snapshots>
         </repository>
     </repositories>
-    <pluginRepositories>
-        <pluginRepository>
-            <id>central-snapshots</id>
-            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-            <snapshots>
-                <enabled>true</enabled>
-            </snapshots>
-        </pluginRepository>
-    </pluginRepositories>
 
     <properties>
         <java.version>17</java.version>
         <org.apache.tika.tika-core.version>2.7.0</org.apache.tika.tika-core.version>
         <org.mapstruct.version>1.5.5.Final</org.mapstruct.version>
         <org.springdoc.version>2.2.0</org.springdoc.version>
-        <cz.cvut.kbss.jopa.version>2.0.0-SNAPSHOT</cz.cvut.kbss.jopa.version>
-        <cz.cvut.kbss.jsonld.version>0.14.2</cz.cvut.kbss.jsonld.version>
-        <org.aspectj.version>1.9.20</org.aspectj.version>
+        <cz.cvut.kbss.jopa.version>2.0.0</cz.cvut.kbss.jopa.version>
+        <cz.cvut.kbss.jsonld.version>0.14.3</cz.cvut.kbss.jsonld.version>
 
         <!-- Default value for deployment type property which should otherwise specified on command line -->
         <deployment>DEV</deployment>
@@ -132,14 +112,14 @@
         <dependency>
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-rio-rdfxml</artifactId>
-            <version>4.3.8</version>
+            <version>4.3.11</version>
         </dependency>
 
         <!-- Spring declarative transactions with JOPA -->
         <dependency>
             <groupId>com.github.ledsoft</groupId>
             <artifactId>jopa-spring-transaction</artifactId>
-            <version>0.3.0-SNAPSHOT</version>
+            <version>0.3.0</version>
         </dependency>
 
         <!-- Spring -->
@@ -177,11 +157,19 @@
             <groupId>org.springframework</groupId>
             <artifactId>spring-aspects</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.retry</groupId>
+            <artifactId>spring-retry</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents.client5</groupId>
             <artifactId>httpclient5</artifactId>
             <version>5.2.1</version>
         </dependency>
+        <dependency>
+            <groupId>org.aspectj</groupId>
+            <artifactId>aspectjrt</artifactId>
+        </dependency>
 
         <!-- JWT support for Java -->
         <dependency>
@@ -427,7 +415,18 @@
                             <artifactId>mapstruct-processor</artifactId>
                             <version>${org.mapstruct.version}</version>
                         </path>
+                        <path>
+                            <groupId>cz.lukaskabc.cvut.processor</groupId>
+                            <artifactId>spring-boot-configuration-docgen-processor</artifactId>
+                            <version>1.0</version>
+                        </path>
                     </annotationProcessorPaths>
+                    <compilerArgs>
+                        <arg>-Aconfigurationdoc.output_file=termit-doc.md</arg>
+                        <arg>-Aconfigurationdoc.format=MD</arg>
+                        <arg>-Aconfigurationdoc.configuration_package=cz.cvut.kbss.termit</arg>
+                        <arg>-Aconfigurationdoc.prepend_required=true</arg>
+                    </compilerArgs>
                     <source>${java.version}</source>
                     <target>${java.version}</target>
                 </configuration>
@@ -448,13 +447,6 @@
                     </aspectLibraries>
                     <parameters>true</parameters>
                 </configuration>
-                <dependencies>
-                    <dependency>
-                        <groupId>org.aspectj</groupId>
-                        <artifactId>aspectjtools</artifactId>
-                        <version>${org.aspectj.version}</version>
-                    </dependency>
-                </dependencies>
                 <executions>
                     <execution>
                         <id>main</id>

diff --git a/src/main/java/cz/cvut/kbss/termit/aspect/ChangeTrackingAspect.java b/src/main/java/cz/cvut/kbss/termit/aspect/ChangeTrackingAspect.java
@@ -46,7 +46,7 @@ public class ChangeTrackingAspect {
     @Autowired
     private ChangeTrackingHelperDao helperDao;
 
-    @Pointcut(value = "execution(public void persist(..)) && target(cz.cvut.kbss.termit.persistence.dao.GenericDao) " +
+    @Pointcut(value = "execution(public void persist(..)) && (target(cz.cvut.kbss.termit.persistence.dao.BaseAssetDao)) " +
             "&& @args(cz.cvut.kbss.termit.model.changetracking.Audited)")
     public void persistOperation() {
     }
@@ -56,7 +56,7 @@ public void persistOperation() {
     public void persistTermOperation() {
     }
 
-    @Pointcut(value = "execution(public * update(..)) && target(cz.cvut.kbss.termit.persistence.dao.GenericDao) " +
+    @Pointcut(value = "execution(public * update(..)) && target(cz.cvut.kbss.termit.persistence.dao.BaseAssetDao) " +
             "&& @args(cz.cvut.kbss.termit.model.changetracking.Audited)")
     public void updateOperation() {
     }

diff --git a/src/main/java/cz/cvut/kbss/termit/config/AppConfig.java b/src/main/java/cz/cvut/kbss/termit/config/AppConfig.java
@@ -23,6 +23,7 @@
 import org.springframework.context.annotation.EnableAspectJAutoProxy;
 import org.springframework.context.annotation.EnableMBeanExport;
 import org.springframework.context.annotation.aspectj.EnableSpringConfigured;
+import org.springframework.retry.annotation.EnableRetry;
 import org.springframework.scheduling.annotation.AsyncConfigurer;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.EnableScheduling;
@@ -33,6 +34,7 @@
 @EnableSpringConfigured
 @EnableAsync
 @EnableScheduling
+@EnableRetry
 public class AppConfig implements AsyncConfigurer {
 
     @Override

diff --git a/src/main/java/cz/cvut/kbss/termit/config/WebAppConfig.java b/src/main/java/cz/cvut/kbss/termit/config/WebAppConfig.java
@@ -24,15 +24,13 @@
 import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import cz.cvut.kbss.jopa.model.MultilingualString;
-import cz.cvut.kbss.jopa.sessions.UnitOfWorkImpl;
 import cz.cvut.kbss.jsonld.JsonLd;
 import cz.cvut.kbss.jsonld.jackson.JsonLdModule;
 import cz.cvut.kbss.jsonld.jackson.serialization.SerializationConstants;
 import cz.cvut.kbss.termit.rest.servlet.DiagnosticsContextFilter;
 import cz.cvut.kbss.termit.util.AdjustedUriTemplateProxyServlet;
 import cz.cvut.kbss.termit.util.ConfigParam;
 import cz.cvut.kbss.termit.util.Constants;
-import cz.cvut.kbss.termit.util.json.ManageableIgnoreMixin;
 import cz.cvut.kbss.termit.util.json.MultilingualStringDeserializer;
 import cz.cvut.kbss.termit.util.json.MultilingualStringSerializer;
 import io.swagger.v3.oas.models.Components;
@@ -94,8 +92,6 @@ public static ObjectMapper createJsonObjectMapper() {
         multilingualStringModule.addSerializer(MultilingualString.class, new MultilingualStringSerializer());
         multilingualStringModule.addDeserializer(MultilingualString.class, new MultilingualStringDeserializer());
         objectMapper.registerModule(multilingualStringModule);
-        // Ignore UoW references injected into entities
-        objectMapper.addMixIn(UnitOfWorkImpl.class, ManageableIgnoreMixin.class);
         // JSR 310 (Java 8 DateTime API)
         objectMapper.registerModule(new JavaTimeModule());
         // Serialize datetime as ISO strings

diff --git a/src/main/java/cz/cvut/kbss/termit/dto/listing/TermDto.java b/src/main/java/cz/cvut/kbss/termit/dto/listing/TermDto.java
@@ -35,7 +35,7 @@
  * Contains fewer data than a regular {@link cz.cvut.kbss.termit.model.Term}.
  */
 @OWLClass(iri = SKOS.CONCEPT)
-@JsonLdAttributeOrder({"uri", "label", "subTerms"})
+@JsonLdAttributeOrder({"uri", "label", "parentTerms", "subTerms"})
 @JsonIgnoreProperties({"definition", "persistenceContext"})
 public class TermDto extends AbstractTerm {
 

diff --git a/src/main/java/cz/cvut/kbss/termit/exception/AnnotationGenerationException.java b/src/main/java/cz/cvut/kbss/termit/exception/AnnotationGenerationException.java
@@ -20,7 +20,7 @@
 /**
  * Indicates a failure during document annotation generation.
  */
-public class AnnotationGenerationException extends TermItException {
+public class AnnotationGenerationException extends FileContentProcessingException {
 
     public AnnotationGenerationException(String message) {
         super(message);

diff --git a/src/main/java/cz/cvut/kbss/termit/exception/FileContentProcessingException.java b/src/main/java/cz/cvut/kbss/termit/exception/FileContentProcessingException.java
@@ -0,0 +1,15 @@
+package cz.cvut.kbss.termit.exception;
+
+/**
+ * Indicates an error when processing file content.
+ */
+public class FileContentProcessingException extends TermItException {
+
+    public FileContentProcessingException(String message) {
+        super(message);
+    }
+
+    public FileContentProcessingException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}
diff --git a/src/main/java/cz/cvut/kbss/termit/model/assignment/OccurrenceTarget.java b/src/main/java/cz/cvut/kbss/termit/model/assignment/OccurrenceTarget.java
@@ -23,6 +23,8 @@
 import cz.cvut.kbss.termit.model.Asset;
 import cz.cvut.kbss.termit.model.selector.Selector;
 import cz.cvut.kbss.termit.util.Vocabulary;
+import jakarta.validation.constraints.NotEmpty;
+import jakarta.validation.constraints.NotNull;
 
 import java.net.URI;
 import java.util.Objects;
@@ -32,10 +34,12 @@
 @OWLClass(iri = Vocabulary.s_c_cil_vyskytu)
 public abstract class OccurrenceTarget extends AbstractEntity {
 
+    @NotNull
     @ParticipationConstraints(nonEmpty = true)
     @OWLObjectProperty(iri = Vocabulary.s_p_ma_zdroj)
     private URI source;
 
+    @NotEmpty
     @ParticipationConstraints(nonEmpty = true)
     @OWLObjectProperty(iri = Vocabulary.s_p_ma_selektor, cascade = CascadeType.ALL, fetch = FetchType.EAGER)
     private Set<Selector> selectors;

diff --git a/src/main/java/cz/cvut/kbss/termit/model/assignment/TermOccurrence.java b/src/main/java/cz/cvut/kbss/termit/model/assignment/TermOccurrence.java
@@ -18,11 +18,18 @@
 package cz.cvut.kbss.termit.model.assignment;
 
 import com.fasterxml.jackson.annotation.JsonTypeInfo;
-import cz.cvut.kbss.jopa.model.annotations.*;
+import cz.cvut.kbss.jopa.model.annotations.CascadeType;
+import cz.cvut.kbss.jopa.model.annotations.FetchType;
+import cz.cvut.kbss.jopa.model.annotations.OWLClass;
+import cz.cvut.kbss.jopa.model.annotations.OWLDataProperty;
+import cz.cvut.kbss.jopa.model.annotations.OWLObjectProperty;
+import cz.cvut.kbss.jopa.model.annotations.ParticipationConstraints;
+import cz.cvut.kbss.jopa.model.annotations.Types;
 import cz.cvut.kbss.jopa.vocabulary.DC;
 import cz.cvut.kbss.termit.model.AbstractEntity;
 import cz.cvut.kbss.termit.model.util.HasTypes;
 import cz.cvut.kbss.termit.util.Vocabulary;
+import jakarta.validation.constraints.NotNull;
 
 import java.net.URI;
 import java.util.Objects;
@@ -37,10 +44,12 @@ public abstract class TermOccurrence extends AbstractEntity implements HasTypes
      */
     public static final String CONTEXT_SUFFIX = "occurrences";
 
+    @NotNull
     @ParticipationConstraints(nonEmpty = true)
     @OWLObjectProperty(iri = Vocabulary.s_p_je_prirazenim_termu)
     private URI term;
 
+    @NotNull
     @ParticipationConstraints(nonEmpty = true)
     @OWLObjectProperty(iri = Vocabulary.s_p_ma_cil, cascade = {CascadeType.MERGE}, fetch = FetchType.EAGER)
     OccurrenceTarget target;
@@ -110,6 +119,35 @@ public void setScore(Double score) {
         this.score = score;
     }
 
+    /**
+     * Marks this term occurrence as suggested by automation.
+     * <p>
+     * Corresponds to classifying with {@link Vocabulary#s_c_navrzeny_vyskyt_termu}.
+     */
+    public void markSuggested() {
+        addType(Vocabulary.s_c_navrzeny_vyskyt_termu);
+    }
+
+    /**
+     * Marks this term occurrence as approved.
+     * <p>
+     * Corresponds to removing the {@link Vocabulary#s_c_navrzeny_vyskyt_termu} type.
+     */
+    public void markApproved() {
+        removeType(Vocabulary.s_c_navrzeny_vyskyt_termu);
+    }
+
+    /**
+     * Checks whether this term occurrence is marked as suggested by automation.
+     * <p>
+     * Suggested in this context means classified with {@link Vocabulary#s_c_navrzeny_vyskyt_termu}.
+     *
+     * @return {@code true} when this instance is marked as suggested by automation
+     */
+    public boolean isSuggested() {
+        return hasType(Vocabulary.s_c_navrzeny_vyskyt_termu);
+    }
+
     @Override
     public String toString() {
         return "TermOccurrence{<" +
@@ -131,7 +169,8 @@ public URI resolveContext() {
     }
 
     /**
-     * Resolves identifier of the repository context in which term occurrences targeting the specified source should be stored.
+     * Resolves identifier of the repository context in which term occurrences targeting the specified source should be
+     * stored.
      * <p>
      * The context is based on the specified source and {@link #CONTEXT_SUFFIX}.
      *

diff --git a/src/main/java/cz/cvut/kbss/termit/model/selector/TextQuoteSelector.java b/src/main/java/cz/cvut/kbss/termit/model/selector/TextQuoteSelector.java
@@ -53,6 +53,12 @@ public TextQuoteSelector(@NotBlank String exactMatch) {
         this.exactMatch = exactMatch;
     }
 
+    public TextQuoteSelector(@NotBlank String exactMatch, String prefix, String suffix) {
+        this.exactMatch = exactMatch;
+        this.prefix = prefix;
+        this.suffix = suffix;
+    }
+
     public String getExactMatch() {
         return exactMatch;
     }

diff --git a/src/main/java/cz/cvut/kbss/termit/persistence/dao/BaseDao.java b/src/main/java/cz/cvut/kbss/termit/persistence/dao/BaseDao.java
@@ -78,6 +78,12 @@ public Optional<T> getReference(URI id) {
         }
     }
 
+    @Override
+    public void detach(T entity) {
+        Objects.requireNonNull(entity);
+        em.detach(entity);
+    }
+
     @ModifiesData
     @Override
     public void persist(T entity) {

diff --git a/src/main/java/cz/cvut/kbss/termit/persistence/dao/GenericDao.java b/src/main/java/cz/cvut/kbss/termit/persistence/dao/GenericDao.java
@@ -60,6 +60,15 @@ public interface GenericDao<T extends HasIdentifier> {
      */
     Optional<T> getReference(URI id);
 
+    /**
+     * Detaches the specified entity from the current persistence context.
+     * <p>
+     * Does nothing if the specified entity is not managed.
+     *
+     * @param entity Entity to detach
+     */
+    void detach(T entity);
+
     /**
      * Persists the specified entity.
      *

diff --git a/src/main/java/cz/cvut/kbss/termit/persistence/dao/TermDao.java b/src/main/java/cz/cvut/kbss/termit/persistence/dao/TermDao.java
@@ -95,11 +95,6 @@ private void postLoad(Term r) {
         r.setInverseExactMatchTerms(loadInverseExactMatchTerms(r));
     }
 
-    public void detach(Term term) {
-        Objects.requireNonNull(term);
-        em.detach(term);
-    }
-
     /**
      * Loads terms whose relatedness to the specified term is inferred due to the symmetry of SKOS related.
      *