Upgrade to spring boot

pom.xml

@@ -86,7 +86,7 @@
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-backend-api</artifactId>
-            <version>2.0.1</version>
+            <version>2.1.0</version>
         </dependency>
         <dependency>
             <groupId>edu.stanford.protege</groupId>

src/main/java/edu/stanford/protege/webprotege/LuceneBeansConfiguration.java

@@ -3,6 +3,7 @@
 import edu.stanford.protege.webprotege.index.*;
 import edu.stanford.protege.webprotege.inject.DataDirectoryProvider;
 import edu.stanford.protege.webprotege.match.EntityMatcherFactory;
+import edu.stanford.protege.webprotege.match.MatcherFactory;
 import edu.stanford.protege.webprotege.project.BuiltInPrefixDeclarations;
 import edu.stanford.protege.webprotege.project.ProjectDisposablesManager;
 import edu.stanford.protege.webprotege.common.ProjectId;
@@ -97,8 +98,9 @@ LuceneIndexImpl luceneIndexImpl(LuceneEntityDocumentTranslator p1,
                                     SearcherManager p2,
                                     LuceneQueryFactory p3,
                                     LuceneDictionaryLanguageValuesMatcher p4,
-                                    QueryAnalyzerFactory p5) {
-        return new LuceneIndexImpl(p1, p2, p3, p4, p5);
+                                    QueryAnalyzerFactory p5,
+                                    MatcherFactory p6) {
+        return new LuceneIndexImpl(p1, p2, p3, p4, p5, p6);
     }
 
     @Bean

src/main/java/edu/stanford/protege/webprotege/ProjectBeansConfiguration.java

@@ -1551,8 +1551,8 @@ CommentPostedSlackWebhookInvoker commentPostedSlackWebhookInvoker(ApplicationNam
     }
 
     @Bean
-    EntitySearcherFactory entitySearcherFactory(ProjectId p1, DictionaryManager p2, EntityNodeRenderer p3) {
-        return new EntitySearcherFactory(p1, p2, p3);
+    EntitySearcherFactory entitySearcherFactory(ProjectId p1, DictionaryManager p2, EntityNodeRenderer p3, MatcherFactory p4) {
+        return new EntitySearcherFactory(p1, p2, p3, p4);
     }
 
     @Bean

src/main/java/edu/stanford/protege/webprotege/entity/EntityLookupRequest.java

@@ -3,6 +3,7 @@
 import com.google.common.base.MoreObjects;
 import com.google.common.collect.ImmutableSet;
 import edu.stanford.protege.webprotege.criteria.CompositeRootCriteria;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
 import edu.stanford.protege.webprotege.search.SearchType;
 import org.semanticweb.owlapi.model.EntityType;
 
@@ -37,7 +38,7 @@ public class EntityLookupRequest implements Serializable {
     private SearchType searchType = SearchType.getDefault();
 
     private ImmutableSet<EntityType<?>> searchedEntityTypes = ImmutableSet.of();
-    
+
     private int searchLimit = DEFAULT_MATCH_LIMIT;
 
 

src/main/java/edu/stanford/protege/webprotege/entity/LookupEntitiesActionHandler.java

@@ -1,12 +1,14 @@
 package edu.stanford.protege.webprotege.entity;
 
 import com.google.common.collect.ImmutableList;
+import com.google.common.collect.ImmutableSet;
 import edu.stanford.protege.webprotege.access.AccessManager;
 import edu.stanford.protege.webprotege.access.BuiltInAction;
 import edu.stanford.protege.webprotege.app.PlaceUrl;
 import edu.stanford.protege.webprotege.common.DictionaryLanguage;
 import edu.stanford.protege.webprotege.common.PageRequest;
 import edu.stanford.protege.webprotege.common.ProjectId;
+import edu.stanford.protege.webprotege.criteria.EntityTypeIsOneOfCriteria;
 import edu.stanford.protege.webprotege.dispatch.AbstractProjectActionHandler;
 import edu.stanford.protege.webprotege.ipc.ExecutionContext;
 import edu.stanford.protege.webprotege.lang.LanguageManager;
@@ -103,7 +105,8 @@ private List<EntityLookupResult> lookupEntities(final EntityLookupRequest entity
         var result = dictionaryManager.getShortFormsContaining(searchStrings,
                                                                entityLookupRequest.getSearchedEntityTypes(),
                                                                languageManager.getLanguages(), ImmutableList.of(),
-                                                               PageRequest.requestFirstPage());
+                                                               PageRequest.requestFirstPage(),
+                EntityTypeIsOneOfCriteria.get(ImmutableSet.copyOf(entityLookupRequest.getSearchedEntityTypes())));
 
         List<EntityLookupResult> lookupResults = new ArrayList<>();
         for (var match : result.getPageElements()) {

src/main/java/edu/stanford/protege/webprotege/search/EntitySearcher.java

@@ -6,7 +6,9 @@
 import com.google.common.collect.ImmutableMap;
 import edu.stanford.protege.webprotege.DataFactory;
 import edu.stanford.protege.webprotege.common.*;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
 import edu.stanford.protege.webprotege.entity.EntityNodeRenderer;
+import edu.stanford.protege.webprotege.match.MatcherFactory;
 import edu.stanford.protege.webprotege.shortform.*;
 import edu.stanford.protege.webprotege.shortform.SearchString;
 import org.semanticweb.owlapi.model.EntityType;
@@ -73,6 +75,10 @@ public class EntitySearcher {
     private final ImmutableList<EntitySearchFilter> searchFilters;
 
     private final EntityNodeRenderer entityNodeRenderer;
+    @Nonnull
+    private final EntityMatchCriteria resultsSetFilter;
+    @Nonnull
+    private final MatcherFactory matcherFactory;
 
 
     public EntitySearcher(@Nonnull ProjectId projectId,
@@ -82,7 +88,9 @@ public EntitySearcher(@Nonnull ProjectId projectId,
                           @Nonnull UserId userId,
                           @Nonnull ImmutableList<DictionaryLanguage> searchLanguages,
                           ImmutableList<EntitySearchFilter> searchFilters,
-                          @Nonnull EntityNodeRenderer entityNodeRenderer) {
+                          @Nonnull EntityNodeRenderer entityNodeRenderer,
+                          @Nonnull EntityMatchCriteria resultsSetFilter,
+                          @Nonnull MatcherFactory matcherFactory) {
         this.projectId = checkNotNull(projectId);
         this.userId = checkNotNull(userId);
         this.dictionaryManager = checkNotNull(dictionaryManager);
@@ -95,6 +103,8 @@ public EntitySearcher(@Nonnull ProjectId projectId,
         this.searchLanguages = checkNotNull(searchLanguages);
         this.searchFilters = checkNotNull(searchFilters);
         this.entityNodeRenderer = entityNodeRenderer;
+        this.resultsSetFilter = resultsSetFilter;
+        this.matcherFactory = checkNotNull(matcherFactory);
     }
 
     public void setPageRequest(@Nonnull PageRequest pageRequest) {
@@ -118,7 +128,8 @@ public void invoke() {
                                                                       entityTypes,
                                                                       searchLanguages,
                                                                       searchFilters,
-                                                                      pageRequest);
+                                                                      pageRequest,
+                resultsSetFilter);
         results = entityMatches.transform(matches -> {
             var entity = matches.getEntity();
             var shortForms = dictionaryManager.getShortForms(entity);

src/main/java/edu/stanford/protege/webprotege/search/EntitySearcherFactory.java

@@ -2,8 +2,11 @@
 
 import com.google.common.collect.ImmutableList;
 import edu.stanford.protege.webprotege.common.DictionaryLanguage;
+import edu.stanford.protege.webprotege.criteria.CompositeRootCriteria;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
 import edu.stanford.protege.webprotege.entity.EntityNodeRenderer;
 import edu.stanford.protege.webprotege.common.ProjectId;
+import edu.stanford.protege.webprotege.match.MatcherFactory;
 import edu.stanford.protege.webprotege.shortform.DictionaryManager;
 import edu.stanford.protege.webprotege.common.UserId;
 import org.semanticweb.owlapi.model.EntityType;
@@ -22,27 +25,34 @@ public class EntitySearcherFactory {
     private final DictionaryManager dictionaryManger;
 
     private final EntityNodeRenderer entityNodeRenderer;
+    private final MatcherFactory matcherFactory;
 
     public EntitySearcherFactory(ProjectId projectId,
                                  DictionaryManager dictionaryManger,
-                                 EntityNodeRenderer entityNodeRenderer) {
+                                 EntityNodeRenderer entityNodeRenderer,
+                                 MatcherFactory matcherFactory) {
         this.projectId = projectId;
         this.dictionaryManger = dictionaryManger;
         this.entityNodeRenderer = entityNodeRenderer;
+        this.matcherFactory = matcherFactory;
     }
 
     public EntitySearcher create(Set<EntityType<?>> entityTypes,
                                  String searchString,
                                  UserId userId,
                                  ImmutableList<DictionaryLanguage> languages,
-                                 ImmutableList<EntitySearchFilter> searchFilters) {
+                                 ImmutableList<EntitySearchFilter> searchFilters,
+                                 EntityMatchCriteria resultsSetFilter) {
         return new EntitySearcher(projectId,
                                   dictionaryManger,
                                   entityTypes,
                                   searchString,
                                   userId,
                                   languages,
                                   searchFilters,
-                                  entityNodeRenderer);
+                                  entityNodeRenderer,
+                resultsSetFilter,
+                matcherFactory
+                );
     }
 }

src/main/java/edu/stanford/protege/webprotege/search/PerformEntitySearchActionHandler.java

@@ -12,6 +12,8 @@
 import edu.stanford.protege.webprotege.dispatch.AbstractProjectActionHandler;
 import edu.stanford.protege.webprotege.ipc.ExecutionContext;
 import edu.stanford.protege.webprotege.lang.LanguageManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.annotation.Nonnull;
 import javax.inject.Inject;
@@ -31,6 +33,8 @@ public class PerformEntitySearchActionHandler extends AbstractProjectActionHandl
     @Nonnull
     private final LanguageManager languageManager;
 
+    private static final Logger logger = LoggerFactory.getLogger(PerformEntitySearchActionHandler.class);
+
     @Inject
     public PerformEntitySearchActionHandler(@Nonnull AccessManager accessManager,
                                             @Nonnull EntitySearcherFactory entitySearcherFactory,
@@ -50,6 +54,7 @@ public Class<PerformEntitySearchAction> getActionClass() {
     @Override
     public PerformEntitySearchResult execute(@Nonnull PerformEntitySearchAction action,
                                              @Nonnull ExecutionContext executionContext) {
+        logger.info("Performing search: {}", action);
         var entityTypes = action.entityTypes();
         var searchString = action.searchString();
         var languages = ImmutableList.<DictionaryLanguage>builder();
@@ -66,7 +71,8 @@ public PerformEntitySearchResult execute(@Nonnull PerformEntitySearchAction acti
                                                           searchString,
                                                           executionContext.userId(),
                                                           languages.build(),
-                                                          searchFilters);
+                                                          searchFilters,
+                action.resultsSetFilter());
         PageRequest pageRequest = action.pageRequest();
         entitySearcher.setPageRequest(pageRequest);
         entitySearcher.invoke();

src/main/java/edu/stanford/protege/webprotege/shortform/DictionaryManager.java

@@ -4,6 +4,7 @@
 import com.google.common.collect.ImmutableMap;
 import edu.stanford.protege.webprotege.common.DictionaryLanguage;
 import edu.stanford.protege.webprotege.common.EntityShortFormMatches;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
 import edu.stanford.protege.webprotege.inject.ProjectSingleton;
 import edu.stanford.protege.webprotege.lang.LanguageManager;
 import edu.stanford.protege.webprotege.common.Page;
@@ -13,6 +14,7 @@
 import org.semanticweb.owlapi.model.OWLEntity;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import javax.inject.Inject;
 import java.util.Collection;
 import java.util.List;
@@ -98,8 +100,9 @@ public Page<EntityShortFormMatches> getShortFormsContaining(@Nonnull List<Search
                                                                 @Nonnull Set<EntityType<?>> entityTypes,
                                                                 @Nonnull List<DictionaryLanguage> languages,
                                                                 @Nonnull ImmutableList<EntitySearchFilter> searchFilters,
-                                                                @Nonnull PageRequest pageRequest) {
-        return dictionary.getShortFormsContaining(searchStrings, entityTypes, languages, searchFilters, pageRequest);
+                                                                @Nonnull PageRequest pageRequest,
+                                                                @Nullable EntityMatchCriteria resultsSetFilter) {
+        return dictionary.getShortFormsContaining(searchStrings, entityTypes, languages, searchFilters, pageRequest, resultsSetFilter);
     }
 
     public void update(@Nonnull Collection<OWLEntity> entities) {

src/main/java/edu/stanford/protege/webprotege/shortform/LuceneIndex.java

@@ -1,12 +1,14 @@
 package edu.stanford.protege.webprotege.shortform;
 
 import edu.stanford.protege.webprotege.common.*;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
 import edu.stanford.protege.webprotege.search.EntitySearchFilter;
 import org.apache.lucene.queryparser.classic.ParseException;
 import org.semanticweb.owlapi.model.EntityType;
 import org.semanticweb.owlapi.model.OWLEntity;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.List;
 import java.util.Optional;
@@ -29,7 +31,8 @@ Optional<Page<EntityShortFormMatches>> search(@Nonnull List<SearchString> queryS
                                                   @Nonnull List<DictionaryLanguage> dictionaryLanguages,
                                                   @Nonnull List<EntitySearchFilter> searchFilters,
                                                   @Nonnull Set<EntityType<?>> entityTypes,
-                                                  @Nonnull PageRequest pageRequest) throws IOException, ParseException;
+                                                  @Nonnull PageRequest pageRequest,
+                                                  @Nullable EntityMatchCriteria resultsSetFilter) throws IOException, ParseException;
 
     /**
      * Finds entities that have the specified short form.

src/main/java/edu/stanford/protege/webprotege/shortform/LuceneIndexImpl.java

@@ -2,6 +2,8 @@
 
 import com.google.common.collect.ImmutableSet;
 import edu.stanford.protege.webprotege.common.*;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
+import edu.stanford.protege.webprotege.match.MatcherFactory;
 import edu.stanford.protege.webprotege.search.EntitySearchFilter;
 import edu.stanford.protege.webprotege.search.EntitySearchFilterId;
 import org.apache.lucene.document.Document;
@@ -15,6 +17,7 @@
 import org.slf4j.LoggerFactory;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import javax.inject.Inject;
 import javax.inject.Provider;
 import java.io.IOException;
@@ -52,18 +55,22 @@ public class LuceneIndexImpl implements LuceneIndex {
 
     @Nonnull
     private final QueryAnalyzerFactory queryAnalyzerFactory;
+    @Nonnull
+    private final MatcherFactory matcherFactory;
 
     @Inject
     public LuceneIndexImpl(@Nonnull LuceneEntityDocumentTranslator luceneEntityDocumentTranslator,
                            @Nonnull SearcherManager searcherManager,
                            @Nonnull LuceneQueryFactory queryFactory,
                            @Nonnull LuceneDictionaryLanguageValuesMatcher luceneDictionaryLanguageValuesMatcher,
-                           @Nonnull QueryAnalyzerFactory queryAnalyzerFactory) {
+                           @Nonnull QueryAnalyzerFactory queryAnalyzerFactory,
+                           @Nonnull MatcherFactory matcherFactory) {
         this.luceneEntityDocumentTranslator = luceneEntityDocumentTranslator;
         this.searcherManager = searcherManager;
         this.queryFactory = queryFactory;
         this.luceneDictionaryLanguageValuesMatcher = luceneDictionaryLanguageValuesMatcher;
         this.queryAnalyzerFactory = queryAnalyzerFactory;
+        this.matcherFactory = matcherFactory;
     }
 
     @Nonnull
@@ -106,7 +113,8 @@ public Optional<Page<EntityShortFormMatches>> search(@Nonnull List<SearchString>
                                                          @Nonnull List<DictionaryLanguage> dictionaryLanguages,
                                                          @Nonnull List<EntitySearchFilter> searchFilters,
                                                          @Nonnull Set<EntityType<?>> entityTypes,
-                                                         @Nonnull PageRequest pageRequest) throws IOException, ParseException {
+                                                         @Nonnull PageRequest pageRequest,
+                                                         @Nullable EntityMatchCriteria resultsSetFilter) throws IOException, ParseException {
         var indexSearcher = searcherManager.acquire();
         //        indexSearcher.setSimilarity(new EntityBasedSimilarity());
         try {
@@ -141,9 +149,13 @@ public Optional<Page<EntityShortFormMatches>> search(@Nonnull List<SearchString>
             var topDocs = indexSearcher.search(query, Integer.MAX_VALUE);
             explain(query, topDocs, indexSearcher);
             var languagesSet = ImmutableSet.copyOf(dictionaryLanguages);
+            var matcher = matcherFactory.getMatcher(resultsSetFilter);
+
             var page = getDictionaryLanguageValues(dictionaryLanguages,
                                                    indexSearcher,
-                                                   topDocs).collect(PageCollector.toPage(pageRequest.getPageNumber(),
+                                                   topDocs)
+                    .filter(p -> matcher.matches(p.getEntity()))
+                    .collect(PageCollector.toPage(pageRequest.getPageNumber(),
                                                                                          pageRequest.getPageSize()));
             return page.map(pg -> pg.transform(entityShortForms -> {
                 var matches = luceneDictionaryLanguageValuesMatcher.getShortFormMatches(entityShortForms,

src/main/java/edu/stanford/protege/webprotege/shortform/MultiLingualDictionaryLuceneImpl.java

@@ -6,11 +6,13 @@
 import edu.stanford.protege.webprotege.common.EntityShortFormMatches;
 import edu.stanford.protege.webprotege.common.Page;
 import edu.stanford.protege.webprotege.common.PageRequest;
+import edu.stanford.protege.webprotege.criteria.EntityMatchCriteria;
 import edu.stanford.protege.webprotege.search.EntitySearchFilter;
 import org.semanticweb.owlapi.model.EntityType;
 import org.semanticweb.owlapi.model.OWLEntity;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import javax.inject.Inject;
 import java.util.List;
 import java.util.Set;
@@ -71,10 +73,11 @@ public Page<EntityShortFormMatches> getShortFormsContaining(@Nonnull List<Search
                                                                 @Nonnull Set<EntityType<?>> entityTypes,
                                                                 @Nonnull List<DictionaryLanguage> languages,
                                                                 @Nonnull ImmutableList<EntitySearchFilter> searchFilters,
-                                                                @Nonnull PageRequest pageRequest) {
+                                                                @Nonnull PageRequest pageRequest,
+                                                                @Nullable EntityMatchCriteria resultsSetFilter) {
         return searchableMultiLingualShortFormDictionary.getShortFormsContaining(searchStrings,
                                                                                  entityTypes,
-                                                                                 languages, searchFilters, pageRequest);
+                                                                                 languages, searchFilters, pageRequest, resultsSetFilter);
     }
 }