Added find by uri

dbrepo-semantics-service/rest-service/src/main/java/at/tuwien/endpoints/QueryEndpoint.java

@@ -15,6 +15,7 @@ import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import io.swagger.v3.oas.annotations.security.SecurityRequirement;
 import jakarta.validation.Valid;
 import jakarta.validation.constraints.NotNull;
+import jakarta.ws.rs.PathParam;
 import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -42,7 +43,7 @@ public class QueryEndpoint {
         this.ontologyService = ontologyService;
     }
 
-    @PostMapping("/ontology/{id}/query")
+    @GetMapping("/ontology/{id}/find/label/{label}")
     @PreAuthorize("hasAuthority('execute-semantic-query')")
     @Timed(value = "semantics.sparql.execute", description = "Time needed to execute a sparql query")
     @Operation(summary = "Register a new ontology", security = @SecurityRequirement(name = "bearerAuth"))
@@ -52,22 +53,50 @@ public class QueryEndpoint {
                     content = {@Content(
                             mediaType = "application/json")}),
     })
-    public ResponseEntity<List<EntityDto>> query(@NotNull @PathVariable("id") Long id,
-                                                 @NotNull @Valid @RequestBody EntitySearchDto data)
+    public ResponseEntity<List<EntityDto>> findByLabel(@NotNull @PathVariable("id") Long id,
+                                                       @NotNull @PathVariable("label") String label)
             throws OntologyNotFoundException, QueryMalformedException {
-        log.debug("endpoint execute query, id={}", id);
+        log.debug("endpoint execute query, id={}, label={}", id, label);
         final Ontology ontology = ontologyService.find(id);
         final List<EntityDto> dtos;
         if (ontology.getSparqlEndpoint() != null) {
-            log.debug("ontology with id {} has SPARQL endpoint", ontology.getId());
-            dtos = sparqlService.find(ontology, data);
+            log.trace("ontology with id {} has SPARQL endpoint", ontology.getId());
+            dtos = sparqlService.findByLabel(ontology, label);
         } else {
-            log.debug("ontology with id {} has RDF fallback", ontology.getId());
-            dtos = rdfService.find(ontology, data);
+            log.trace("ontology with id {} has RDF fallback", ontology.getId());
+            dtos = rdfService.findByLabel(ontology, label);
         }
         log.trace("create ontology resulted in dtos {}", dtos);
         return ResponseEntity.ok()
                 .body(dtos);
     }
 
+    @GetMapping("/ontology/{id}/find/uri/{uri}")
+    @PreAuthorize("hasAuthority('execute-semantic-query')")
+    @Timed(value = "semantics.sparql.execute", description = "Time needed to execute a sparql query")
+    @Operation(summary = "Register a new ontology", security = @SecurityRequirement(name = "bearerAuth"))
+    @ApiResponses(value = {
+            @ApiResponse(responseCode = "200",
+                    description = "Executed sparql query successfully",
+                    content = {@Content(
+                            mediaType = "application/json")}),
+    })
+    public ResponseEntity<EntityDto> findByUri(@NotNull @PathVariable("id") Long id,
+                                               @NotNull @PathVariable("uri") String uri)
+            throws OntologyNotFoundException, QueryMalformedException {
+        log.debug("endpoint execute query, id={}, uri={}", id, uri);
+        final Ontology ontology = ontologyService.find(id);
+        final EntityDto dto;
+        if (ontology.getSparqlEndpoint() != null) {
+            log.trace("ontology with id {} has SPARQL endpoint", ontology.getId());
+            dto = sparqlService.findByUri(ontology, uri);
+        } else {
+            log.trace("ontology with id {} has RDF fallback", ontology.getId());
+            dto = rdfService.findByUri(ontology, uri);
+        }
+        log.trace("create ontology resulted in dto {}", dto);
+        return ResponseEntity.ok()
+                .body(dto);
+    }
+
 }

dbrepo-semantics-service/rest-service/src/main/resources/application-local.yml

@@ -43,7 +43,7 @@ logging:
 fda:
   ready.path: ./ready
   jwt:
-    issuer: http://localhost/realms/dbrepo
+    issuer: http://localhost:8080/realms/dbrepo
     public_key: MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB
   client_secret: client-secret
   client_id: dbrepo-client

dbrepo-semantics-service/services/src/main/java/at/tuwien/service/QueryService.java

@@ -9,7 +9,9 @@ import java.util.List;
 
 public interface QueryService {
 
-    List<EntityDto> find(Ontology ontology, EntitySearchDto query) throws QueryMalformedException;
+    List<EntityDto> findByLabel(Ontology ontology, String label) throws QueryMalformedException;
 
-    List<EntityDto> find(Ontology ontology, EntitySearchDto query, Integer limit) throws QueryMalformedException;
+    List<EntityDto> findByLabel(Ontology ontology, String label, Integer limit) throws QueryMalformedException;
+
+    EntityDto findByUri(Ontology ontology, String uri) throws QueryMalformedException;
 }

dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/RdfServiceImpl.java

@@ -8,10 +8,12 @@ import at.tuwien.service.QueryService;
 import lombok.extern.log4j.Log4j2;
 import org.apache.jena.query.*;
 import org.apache.jena.rdfconnection.RDFConnection;
+import org.apache.jena.riot.RiotException;
 import org.apache.jena.shared.JenaException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
 
@@ -27,16 +29,16 @@ public class RdfServiceImpl implements QueryService {
     }
 
     @Override
-    public List<EntityDto> find(Ontology ontology, EntitySearchDto query) throws QueryMalformedException {
-        return find(ontology, query, 10);
+    public List<EntityDto> findByLabel(Ontology ontology, String label) throws QueryMalformedException {
+        return findByLabel(ontology, label, 10);
     }
 
     @Override
-    public List<EntityDto> find(Ontology ontology, EntitySearchDto query, Integer limit) throws QueryMalformedException {
+    public List<EntityDto> findByLabel(Ontology ontology, String label, Integer limit) throws QueryMalformedException {
         final String statement = String.join("\n",
                 "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
                 "SELECT ?o ?label {",
-                "  ?o rdfs:label \"" + query.getLabel().replace("\"", "") + "\"@en .",
+                "  ?o rdfs:label \"" + label.replace("\"", "") + "\"@en .",
                 "  ?o rdfs:label ?label .",
                 "  FILTER (langMatches(lang(?label), \"EN\" ) )",
                 "} LIMIT " + limit);
@@ -59,4 +61,36 @@ public class RdfServiceImpl implements QueryService {
             throw new QueryMalformedException("Failed to parse query: " + e.getMessage(), e);
         }
     }
+
+    @Override
+    public EntityDto findByUri(Ontology ontology, String uri) throws QueryMalformedException {
+        final String statement = String.join("\n",
+                "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
+                "SELECT ?label {",
+                "  <" + uri + "> rdfs:label ?label .",
+                "  FILTER (langMatches(lang(?label), \"EN\" ) )",
+                "} LIMIT 1");
+        log.trace("compiled local query {}", statement);
+        final RDFConnection conn = RDFConnection.connect(this.dataset);
+        conn.load(ontology.getLocal());
+        final List<EntityDto> results = new LinkedList<>();
+        try {
+            conn.querySelect(statement, (qs) -> {
+                final EntityDto entity = EntityDto.builder()
+                        .uri(qs.getResource("o").toString())
+                        .label(qs.getLiteral("label").getLexicalForm())
+                        .build();
+                results.add(entity);
+            });
+            conn.close();
+        } catch (JenaException e) {
+            log.error("Failed to parse query: {}", e.getMessage());
+            throw new QueryMalformedException("Failed to parse query: " + e.getMessage(), e);
+        }
+        if (results.size() != 1) {
+            log.error("Failed to find label: did not produce a result for uri {}", uri);
+            throw new QueryMalformedException("Failed to find uri: did not produce a result for uri " + uri);
+        }
+        return results.get(0);
+    }
 }

dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/SparqlServiceImpl.java

 package at.tuwien.service.impl;
 
 import at.tuwien.api.semantics.EntityDto;
-import at.tuwien.api.semantics.EntitySearchDto;
 import at.tuwien.entities.semantics.Ontology;
 import at.tuwien.exception.QueryMalformedException;
 import at.tuwien.repository.jpa.OntologyRepository;
@@ -53,18 +52,18 @@ public class SparqlServiceImpl implements QueryService {
     }
 
     @Override
-    public List<EntityDto> find(Ontology ontology, EntitySearchDto query) throws QueryMalformedException {
-        return find(ontology, query, 10);
+    public List<EntityDto> findByLabel(Ontology ontology, String label) throws QueryMalformedException {
+        return findByLabel(ontology, label, 10);
     }
 
     @Override
-    public List<EntityDto> find(Ontology ontology, EntitySearchDto query, Integer limit) throws QueryMalformedException {
+    public List<EntityDto> findByLabel(Ontology ontology, String label, Integer limit) throws QueryMalformedException {
         final String statement = String.join("\n",
                 "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
                 "SELECT * {",
                 "  SERVICE <" + ontology.getSparqlEndpoint() + "> {",
                 "    SELECT ?o ?label {",
-                "      ?o rdfs:label \"" + query.getLabel().replace("\"", "") + "\"@en .",
+                "      ?o rdfs:label \"" + label.replace("\"", "") + "\"@en .",
                 "      ?o rdfs:label ?label .",
                 "      FILTER (langMatches(lang(?label), \"EN\" ) )",
                 "     } LIMIT " + limit,
@@ -89,4 +88,35 @@ public class SparqlServiceImpl implements QueryService {
         return results;
     }
 
+    @Override
+    public EntityDto findByUri(Ontology ontology, String uri) throws QueryMalformedException {
+        final String statement = String.join("\n",
+                "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
+                "SELECT * {",
+                "  SERVICE <" + ontology.getSparqlEndpoint() + "> {",
+                "    SELECT ?label {",
+                "      <" + uri + "> rdfs:label ?label .",
+                "      FILTER (langMatches(lang(?label), \"EN\" ) )",
+                "     } LIMIT 1",
+                "  }",
+                "}");
+        log.trace("compiled remote query {}", statement);
+        try (QueryExecution execution = QueryExecutionFactory.create(statement, this.dataset.getDefaultModel())) {
+            final Iterator<QuerySolution> resultSet = execution.execSelect();
+            while (resultSet.hasNext()) {
+                final QuerySolution solution = resultSet.next();
+                final EntityDto entity = EntityDto.builder()
+                        .uri(solution.get("o").toString())
+                        .label(solution.get("label").asLiteral().getLexicalForm())
+                        .build();
+                return entity;
+            }
+        } catch (QueryParseException | IllegalArgumentException | RiotException e) {
+            log.error("Failed to parse query: {}", e.getMessage());
+            throw new QueryMalformedException("Failed to parse query: " + e.getMessage(), e);
+        }
+        log.error("Failed to find label: did not produce a result for uri {}", uri);
+        throw new QueryMalformedException("Failed to find uri: did not produce a result for uri " + uri);
+    }
+
 }

dbrepo-semantics-service/services/src/main/java/at/tuwien/service/impl/TableServiceImpl.java

@@ -54,12 +54,9 @@ public class TableServiceImpl implements TableService {
         final Table table = find(databaseId, tableId);
         final List<TableColumnEntityDto> suggestions = new LinkedList<>();
         for (TableColumn column : table.getColumns()) {
-            final EntitySearchDto search = EntitySearchDto.builder()
-                    .label(column.getName())
-                    .build();
             for (Ontology ontology : ontologyService.findAll()) {
                 final QueryService service = ontology.getSparqlEndpoint() != null ? sparqlService : rdfService;
-                suggestions.addAll(service.find(ontology, search, 3)
+                suggestions.addAll(service.findByLabel(ontology, column.getName(), 3)
                         .stream()
                         .map(e -> TableColumnEntityDto.builder()
                                 .databaseId(databaseId)