Merge remote-tracking branch 'upstream/master' into upstream-merge

# Conflicts:
#	ontology/termit-glosář.ttl
#	ontology/termit-model.ttl
#	pom.xml
#	src/test/java/cz/cvut/kbss/termit/service/repository/BaseAssetRepositoryServiceTest.java

README.md

@@ -126,11 +126,13 @@ Build configuration and deployment is described in [setup.md](doc/setup.md).
 ## Dockerization
 
 The docker image of TermIt backend can be built by 
-`docker build -t kbss-cvut:termit .` 
-An optional argument is `REPOSITORY_URL` pointing to the RDF4J/GraphDB repository.
+`docker build -t termit-server .` 
 
 Then, TermIt can be run and exposed at the port 8080 as 
-`sudo docker run -p 8080:8080 kbss-cvut:termit`
+`sudo docker run -e REPOSITORY_URL=<GRAPHDB_REPOSITORY_URL> -p 8080:8080 termit-server`
+
+An optional argument is `<GRAPHDB_REPOSITORY_URL>` pointing to the RDF4J/GraphDB repository.
+
 
 ## License
 

ontology/termit-glosář.ttl

@@ -469,3 +469,12 @@ termit-pojem:je-publikován
                 termit:glosář ;
         <http://www.w3.org/2004/02/skos/core#prefLabel>
                 "Is published"@en , "Je publikován"@cs .
+
+termit-pojem:má-můj-poslední-komentář
+        a       <http://www.w3.org/2004/02/skos/core#Concept> ;
+        <http://www.w3.org/2004/02/skos/core#broader>
+                <https://slovník.gov.cz/základní/pojem/vlastnost> , <https://slovník.gov.cz/základní/pojem/typ-vlastnosti> ;
+        <http://www.w3.org/2004/02/skos/core#inScheme>
+                termit:glosář ;
+        <http://www.w3.org/2004/02/skos/core#prefLabel>
+                "Has my last comment"@en , "Má můj poslední komentář"@cs .

ontology/termit-model.ttl

@@ -52,14 +52,14 @@ termit-pojem:uživatel-termitu
 termit-pojem:má-zdroj-definice-termu
         a                   owl:ObjectProperty , <https://slovník.gov.cz/základní/pojem/typ-vztahu> ;
         rdfs:domain         <http://onto.fel.cvut.cz/ontologies/slovník/agendový/popis-dat/pojem/term> ;
-        rdfs:range          xsd:boolean ;
-        rdfs:subPropertyOf  <https://slovník.gov.cz/základní/pojem/vlastnost> .
+        rdfs:range          termit-pojem:zdroj-definice-termu ;
+        rdfs:subPropertyOf  <https://slovník.gov.cz/základní/pojem/vztah> .
 
 termit-pojem:je-draft
         a                   owl:DatatypeProperty , <https://slovník.gov.cz/základní/pojem/typ-vlastnosti> ;
         rdfs:domain         <http://onto.fel.cvut.cz/ontologies/slovník/agendový/popis-dat/pojem/term> ;
-        rdfs:range          termit-pojem:zdroj-definice-termu ;
-        rdfs:subPropertyOf  <https://slovník.gov.cz/základní/pojem/vztah> .
+        rdfs:range          xsd:boolean ;
+        rdfs:subPropertyOf  <https://slovník.gov.cz/základní/pojem/vlastnost> .
 
 <http://onto.fel.cvut.cz/ontologies/slovník/agendový/popis-dat/pojem/term>
         a       owl:Class .
@@ -264,3 +264,6 @@ termit-pojem:je-publikován
         a               owl:DatatypeProperty , <https://slovník.gov.cz/základní/pojem/typ-vlastnosti> ;
         rdfs:domain         <http://onto.fel.cvut.cz/ontologies/slovník/agendový/popis-dat/pojem/term> ;
         rdfs:subPropertyOf  <https://slovník.gov.cz/základní/pojem/vlastnost> .
+
+termit-pojem:má-můj-poslední-komentář
+        a               owl:ObjectProperty.

pom.xml

@@ -11,7 +11,7 @@
     </parent>
 
     <artifactId>termit</artifactId>
-    <version>2.4.0</version>
+    <version>2.4.1</version>
     <name>TermIt</name>
     <description>Terminology manager based on Semantic Web technologies.</description>
     <packaging>${packaging}</packaging>
@@ -38,6 +38,7 @@
         <!-- Default value for deployment type property which should otherwise specified on command line -->
         <deployment>DEV</deployment>
         <packaging>jar</packaging>
+        <org.apache.tika.tika-core.version>1.26</org.apache.tika.tika-core.version>
         <!-- Do not activate any Spring profiles by default -->
         <spring.profiles.active/>
     </properties>
@@ -92,6 +93,13 @@
             <version>1.11</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/org.apache.tika/tika-core -->
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-core</artifactId>
+            <version>${org.apache.tika.tika-core.version}</version>
+        </dependency>
+
         <!-- JOPA -->
         <dependency>
             <groupId>cz.cvut.kbss.jopa</groupId>

src/main/java/cz/cvut/kbss/termit/config/WebAppConfig.java

@@ -20,12 +20,14 @@
 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.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 org.springframework.boot.web.servlet.FilterRegistrationBean;
@@ -79,12 +81,14 @@ public ObjectMapper objectMapper() {
      */
     public static ObjectMapper createJsonObjectMapper() {
         final ObjectMapper objectMapper = new ObjectMapper();
-        objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+        objectMapper.setSerializationInclusion(JsonInclude.Include.ALWAYS);
         objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
         final SimpleModule multilingualStringModule = new SimpleModule();
         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());
         return objectMapper;

src/main/java/cz/cvut/kbss/termit/dto/RecentlyCommentedAsset.java

@@ -21,6 +21,7 @@
         variables = {
             @VariableResult(name = "entity", type = URI.class),
             @VariableResult(name = "lastCommentUri", type = URI.class),
+            @VariableResult(name = "myLastCommentUri", type = URI.class),
             @VariableResult(name = "type", type = String.class)
         })})
 public class RecentlyCommentedAsset implements Serializable {
@@ -34,15 +35,22 @@ public class RecentlyCommentedAsset implements Serializable {
     @OWLObjectProperty(iri = Vocabulary.s_p_je_tematem)
     private Comment lastComment;
 
+    @Transient
+    private URI myLastCommentUri;
+
+    @OWLObjectProperty(iri = Vocabulary.s_p_ma_muj_posledni_komentar)
+    private Comment myLastComment;
+
     @Types
     private Set<String> types;
 
     public RecentlyCommentedAsset() {
     }
 
-    public RecentlyCommentedAsset(URI entity, URI lastCommentUri, String type) {
+    public RecentlyCommentedAsset(URI entity, URI lastCommentUri, URI myLastCommentUri, String type) {
         this.uri = entity;
         this.lastCommentUri = lastCommentUri;
+        this.myLastCommentUri = myLastCommentUri;
         this.types = new HashSet<>(Collections.singleton(type));
     }
 
@@ -79,11 +87,29 @@ public RecentlyCommentedAsset setLastComment(Comment lastComment) {
         return this;
     }
 
+    public URI getMyLastCommentUri() {
+        return myLastCommentUri;
+    }
+
+    public void setMyLastCommentUri(URI myLastCommentUri) {
+        this.myLastCommentUri = myLastCommentUri;
+    }
+
+    public Comment getMyLastComment() {
+        return myLastComment;
+    }
+
+    public RecentlyCommentedAsset setMyLastComment(Comment myLastComment) {
+        this.myLastComment = myLastComment;
+        return this;
+    }
+
     @Override
     public String toString() {
         return "RecentlyCommentedAsset{" +
             "uri=" + uri +
-            ", comment=" + lastComment.toString() +
+            ", comment=" + lastComment +
+            ", myLastComment=" + myLastComment +
             ", types=" + types +
             '}';
     }
@@ -99,11 +125,12 @@ public boolean equals(Object o) {
         RecentlyCommentedAsset that = (RecentlyCommentedAsset) o;
         return Objects.equals(uri, that.uri) &&
             Objects.equals(lastComment, that.lastComment) &&
+            Objects.equals(myLastComment, that.myLastComment) &&
             Objects.equals(types, that.types);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(uri, lastComment, types);
+        return Objects.hash(uri, lastComment, myLastComment, types);
     }
 }

src/main/java/cz/cvut/kbss/termit/event/DocumentRenameEvent.java

@@ -0,0 +1,34 @@
+package cz.cvut.kbss.termit.event;
+
+import cz.cvut.kbss.termit.model.resource.Document;
+import java.util.Objects;
+import org.springframework.context.ApplicationEvent;
+
+/**
+ * Indicates that a {@link Document} asset has changed its label.
+ */
+public class DocumentRenameEvent extends ApplicationEvent {
+
+    private final String originalName;
+
+    private final String newName;
+
+    public DocumentRenameEvent(Document source, String originalName, String newName) {
+        super(source);
+        this.originalName = Objects.requireNonNull(originalName);
+        this.newName = Objects.requireNonNull(newName);
+    }
+
+    public String getOriginalName() {
+        return originalName;
+    }
+
+    public String getNewName() {
+        return newName;
+    }
+
+    @Override
+    public Document getSource() {
+        return (Document) super.getSource();
+    }
+}

src/main/java/cz/cvut/kbss/termit/persistence/dao/AssetDao.java

@@ -184,7 +184,7 @@ List<URI> findUniqueLastModifiedEntitiesBy(User author, int limit) {
     public List<RecentlyCommentedAsset> findLastCommented(int limit) {
         try {
             return (List<RecentlyCommentedAsset>) em
-                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?type"
+                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?myLastCommentUri ?type"
                     + " WHERE { ?lastCommentUri a ?commentType ;"
                     + "           ?hasEntity ?entity ."
                     + "  OPTIONAL { ?lastCommentUri ?hasModifiedTime ?modified . }"
@@ -226,12 +226,24 @@ public List<RecentlyCommentedAsset> findLastCommented(int limit) {
     public List<RecentlyCommentedAsset> findLastCommentedInReaction(User author, int limit) {
         try {
             return (List<RecentlyCommentedAsset>) em
-                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?type"
+                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?myLastCommentUri ?type"
                     + " WHERE { ?lastCommentUri a ?commentType ;"
                     + "           ?hasEntity ?entity ."
-                    + "  FILTER EXISTS { ?comment3 ?hasEntity ?entity ;"
-                    + "                            ?hasAuthor ?author . "
-                    + "                  FILTER(?comment3 != ?lastCommentUri)}"
+                    + "         ?myLastCommentUri ?hasEntity ?entity ;"
+                    + "                           ?hasAuthor ?author . "
+                    + "         OPTIONAL { ?myLastCommentUri ?hasModifiedTime ?modifiedByMe . } "
+                    + "         OPTIONAL { ?myLastCommentUri ?hasCreatedByMe  ?createdByMe . } "
+                    + "         BIND(COALESCE(?modifiedByMe,?createdByMe) AS ?lastCommentedByMe) "
+                    + " { SELECT (MAX(?lastCommentedByMe2) AS ?maxByMe) {"
+                    + "         ?commentByMe ?hasEntity ?entity ; "
+                    + "                      ?hasAuthor ?author . "
+                    + "          OPTIONAL { ?commentByMe ?hasModifiedTime ?modifiedByMe2 . } "
+                    + "          OPTIONAL { ?commentByMe ?hasCreatedTime ?createdByMe2 . } "
+                    + "          BIND(COALESCE(?modifiedByMe2,?createdByMe2) AS ?lastCommentedByMe2) "
+                    + "        } GROUP BY ?entity "
+                    + "  }"
+                    + "  FILTER (?lastCommentedByMe = ?maxByMe )"
+                    + "  FILTER(?myLastCommentUri != ?lastCommentUri)"
                     + "  OPTIONAL { ?lastCommentUri ?hasModifiedTime ?modified . }"
                     + "  OPTIONAL { ?lastCommentUri ?hasCreatedTime ?created . }"
                     + "  BIND(COALESCE(?modified,?created) AS ?lastCommented) "
@@ -257,7 +269,8 @@ public List<RecentlyCommentedAsset> findLastCommentedInReaction(User author, int
                 .setMaxResults(limit).getResultStream()
                 .map(r -> {
                         final RecentlyCommentedAsset a = (RecentlyCommentedAsset) r;
-                        return a.setLastComment(em.find(Comment.class, a.getLastCommentUri()));
+                        return a.setLastComment(em.find(Comment.class, a.getLastCommentUri()))
+                            .setMyLastComment(em.find(Comment.class, a.getMyLastCommentUri()));
                     }
                 ).collect(Collectors.toList());
         } catch (RuntimeException e) {
@@ -273,7 +286,7 @@ public List<RecentlyCommentedAsset> findLastCommentedInReaction(User author, int
     public List<RecentlyCommentedAsset> findMyLastCommented(User author, int limit) {
         try {
             return (List<RecentlyCommentedAsset>) em
-                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?type"
+                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?myLastCommentUri ?type"
                     + " WHERE { ?lastCommentUri a ?commentType ;"
                     + "           ?hasEntity ?entity ."
                     + "        FILTER EXISTS{ ?x ?hasModifiedEntity ?entity ;"
@@ -312,51 +325,6 @@ public List<RecentlyCommentedAsset> findMyLastCommented(User author, int limit)
         }
     }
 
-    /**
-     * Finds unique assets last commented by me.
-     * @param limit max number of entities
-     * @return list
-     */
-    public List<RecentlyCommentedAsset> findLastCommentedByMe(User author, int limit) {
-        try {
-            return (List<RecentlyCommentedAsset>) em
-                .createNativeQuery("SELECT DISTINCT ?entity ?lastCommentUri ?type"
-                    + " WHERE { ?lastCommentUri a ?commentType ;"
-                    + "           ?hasEntity ?entity ;"
-                    + "           ?hasCreator ?author ."
-                    + "  OPTIONAL { ?lastCommentUri ?hasModifiedTime ?modified . }"
-                    + "  OPTIONAL { ?lastCommentUri ?hasCreatedTime ?created . }"
-                    + "  BIND(COALESCE(?modified,?created) AS ?lastCommented) "
-                    + "  BIND(?cls as ?type) "
-                    + "  { SELECT (MAX(?lastCommented2) AS ?max) {"
-                    + "           ?comment2 ?hasEntity ?entity ."
-                    + "           OPTIONAL { ?comment2 ?hasModifiedTime ?modified2 . }"
-                    + "           OPTIONAL { ?comment2 ?hasCreatedTime ?created2 . }"
-                    + "           BIND(COALESCE(?modified2,?created2) AS ?lastCommented2) "
-                    + "        } GROUP BY ?entity"
-                    + "  }"
-                    + "  FILTER (?lastCommented = ?max )"
-                    + "} ORDER BY DESC(?lastCommented) ", "RecentlyCommentedAsset")
-                .setParameter("cls", typeUri)
-                .setParameter("commentType", URI.create(Vocabulary.s_c_Comment))
-                .setParameter("hasEntity", URI.create(Vocabulary.s_p_topic))
-                .setParameter("hasCreator", URI.create(Vocabulary.s_p_has_creator))
-                .setParameter("author", author)
-                .setParameter("hasModifiedTime",
-                    URI.create(Vocabulary.s_p_ma_datum_a_cas_posledni_modifikace))
-                .setParameter("hasCreatedTime",
-                    URI.create(Vocabulary.s_p_ma_datum_a_cas_vytvoreni))
-                .setMaxResults(limit).getResultStream()
-                .map(r -> {
-                        final RecentlyCommentedAsset a = (RecentlyCommentedAsset) r;
-                        return a.setLastComment(em.find(Comment.class, a.getLastCommentUri()));
-                    }
-                ).collect(Collectors.toList());
-        } catch (RuntimeException e) {
-            throw new PersistenceException(e);
-        }
-    }
-
     /**
      * Identifier of an RDF property representing this assets label.
      *

src/main/java/cz/cvut/kbss/termit/rest/AssetController.java

@@ -63,10 +63,4 @@ public List<RecentlyCommentedAsset> getMyLastCommented(
         @RequestParam(name = "limit", required = false, defaultValue = DEFAULT_LIMIT) int limit) {
         return assetService.findMyLastCommented(limit);
     }
-
-    @RequestMapping(value = "/last-commented-by-me", produces = {MediaType.APPLICATION_JSON_VALUE, JsonLd.MEDIA_TYPE})
-    public List<RecentlyCommentedAsset> getLastCommentedByMe(
-        @RequestParam(name = "limit", required = false, defaultValue = DEFAULT_LIMIT) int limit) {
-        return assetService.findLastCommentedByMe(limit);
-    }
 }

src/main/java/cz/cvut/kbss/termit/service/business/AssetService.java

@@ -150,19 +150,6 @@ public List<RecentlyCommentedAsset> findMyLastCommented(int limit) {
         return result.subList(0, Math.min(result.size(), limit));
     }
 
-    /**
-     * Finds the specified number of assets most recently commented by me.
-     *
-     * @param limit Maximum number of assets to retrieve
-     * @return List of recently commented assets
-     */
-    public List<RecentlyCommentedAsset> findLastCommentedByMe(int limit) {
-        ensureValidLimitForLastCommented(limit);
-        final User me = securityUtils.getCurrentUser().toUser();
-        final List<RecentlyCommentedAsset> result = termRepositoryService.findLastCommentedByMe(me, limit);
-        return result.subList(0, Math.min(result.size(), limit));
-    }
-
     private void ensureValidLimitForLastCommented(int limit) {
         if (limit < 0) {
             throw new IllegalArgumentException("Maximum for recently commented assets must not be less than 0.");