Merge pull request #1568 from thehyve/refactoring/FAIRSPC-79

Refactoring/fairspc 79

projects/saturn/src/main/java/io/fairspace/saturn/config/KeycloakConfig.java

@@ -0,0 +1,32 @@
+package io.fairspace.saturn.config;
+
+import org.keycloak.OAuth2Constants;
+import org.keycloak.admin.client.Keycloak;
+import org.keycloak.admin.client.KeycloakBuilder;
+import org.keycloak.admin.client.resource.UsersResource;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import io.fairspace.saturn.config.properties.KeycloakClientProperties;
+
+@Configuration
+public class KeycloakConfig {
+
+    @Bean
+    public UsersResource usersResource(Keycloak keycloak, KeycloakClientProperties keycloakClientProperties) {
+        return keycloak.realm(keycloakClientProperties.getRealm()).users();
+    }
+
+    @Bean
+    public Keycloak keycloak(KeycloakClientProperties keycloakClientProperties) {
+        return KeycloakBuilder.builder()
+                .serverUrl(keycloakClientProperties.getAuthServerUrl())
+                .realm(keycloakClientProperties.getRealm())
+                .grantType(OAuth2Constants.CLIENT_CREDENTIALS)
+                .clientId(keycloakClientProperties.getClientId())
+                .clientSecret(keycloakClientProperties.getClientSecret())
+                .username(keycloakClientProperties.getClientId())
+                .password(keycloakClientProperties.getClientSecret())
+                .build();
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/config/MappingConfig.java

@@ -0,0 +1,35 @@
+package io.fairspace.saturn.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+
+import io.fairspace.saturn.services.IRIModule;
+
+import static com.fasterxml.jackson.databind.DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES;
+import static com.fasterxml.jackson.databind.SerializationFeature.WRITE_DATES_AS_TIMESTAMPS;
+
+@Configuration
+public class MappingConfig {
+
+    /**
+     * The maapper is used to read views.yaml configuration file
+     */
+    @Bean
+    public ObjectMapper yamlObjectMapper() {
+        return new ObjectMapper(new YAMLFactory());
+    }
+
+    @Bean
+    @Primary // to be used by default, including serialization of JSON responses to HTTP requests
+    public ObjectMapper jsonObjectMapper() {
+        return new ObjectMapper()
+                .registerModule(new IRIModule())
+                .registerModule(new JavaTimeModule())
+                .configure(WRITE_DATES_AS_TIMESTAMPS, false)
+                .configure(FAIL_ON_UNKNOWN_PROPERTIES, false);
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/config/MetadataConfig.java

@@ -0,0 +1,38 @@
+package io.fairspace.saturn.config;
+
+import org.apache.jena.query.Dataset;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.sparql.util.Symbol;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import io.fairspace.saturn.rdf.transactions.Transactions;
+import io.fairspace.saturn.services.metadata.MetadataPermissions;
+import io.fairspace.saturn.services.metadata.MetadataService;
+import io.fairspace.saturn.services.metadata.validation.ComposedValidator;
+
+@Configuration
+public class MetadataConfig {
+
+    public static final Symbol METADATA_SERVICE = Symbol.create("metadata_service");
+
+    @Bean
+    public MetadataService metadataService(
+            Transactions transactions,
+            MetadataPermissions metadataPermissions,
+            @Qualifier("dataset") Dataset dataset,
+            @Qualifier("vocabulary") Model vocabulary,
+            @Qualifier("systemVocabulary") Model systemVocabulary,
+            @Qualifier("composedValidator") ComposedValidator composedValidator) {
+        var metadataService =
+                new MetadataService(transactions, vocabulary, systemVocabulary, composedValidator, metadataPermissions);
+        // This is a workaround (old, not a new one) to resolve circular dependency:
+        // MetadataService --> ComposedValidator --> URIPrefixValidator --> DavFactory --> DirectoryResource -->
+        // MetadataService
+        // TODO: refactor to avoid circular dependency and !!!USE!!! injection using Spring (at least in DavFactory)
+        //  this to-do supposes getting rid of the following line and using dataset context for storing metadataService
+        dataset.getContext().set(METADATA_SERVICE, metadataService);
+        return metadataService;
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/config/RdfModelConfig.java

@@ -0,0 +1,28 @@
+package io.fairspace.saturn.config;
+
+import org.apache.jena.rdf.model.Model;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import static org.apache.jena.riot.RDFDataMgr.loadModel;
+
+@Configuration
+public class RdfModelConfig {
+
+    @Bean
+    public Model systemVocabulary() {
+        return loadModel("system-vocabulary.ttl");
+    }
+
+    @Bean
+    public Model userVocabulary() {
+        return loadModel("vocabulary.ttl");
+    }
+
+    @Bean
+    public Model vocabulary(
+            @Qualifier("systemVocabulary") Model systemVocabulary, @Qualifier("userVocabulary") Model userVocabulary) {
+        return systemVocabulary.union(userVocabulary);
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/config/RdfStorageConfig.java

@@ -0,0 +1,36 @@
+package io.fairspace.saturn.config;
+
+import org.apache.jena.query.Dataset;
+import org.apache.jena.sparql.core.DatasetImpl;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.lang.Nullable;
+
+import io.fairspace.saturn.config.properties.JenaProperties;
+import io.fairspace.saturn.config.properties.ViewsProperties;
+import io.fairspace.saturn.rdf.SaturnDatasetFactory;
+import io.fairspace.saturn.rdf.search.FilteredDatasetGraph;
+import io.fairspace.saturn.services.metadata.MetadataPermissions;
+import io.fairspace.saturn.services.views.ViewStoreClientFactory;
+
+@Configuration
+public class RdfStorageConfig {
+
+    @Value("${application.publicUrl}")
+    private String publicUrl;
+
+    @Bean
+    public Dataset dataset(
+            ViewsProperties viewsProperties,
+            JenaProperties jenaProperties,
+            @Nullable ViewStoreClientFactory viewStoreClientFactory) {
+        return SaturnDatasetFactory.connect(viewsProperties, jenaProperties, viewStoreClientFactory, publicUrl);
+    }
+
+    @Bean
+    public Dataset filteredDataset(Dataset dataset, MetadataPermissions metadataPermissions) {
+        var filteredDatasetGraph = new FilteredDatasetGraph(dataset.asDatasetGraph(), metadataPermissions);
+        return DatasetImpl.wrap(filteredDatasetGraph);
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/config/SecondaryStorageConfig.java

@@ -0,0 +1,33 @@
+package io.fairspace.saturn.config;
+
+import javax.sql.DataSource;
+
+import com.zaxxer.hikari.HikariConfig;
+import com.zaxxer.hikari.HikariDataSource;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import io.fairspace.saturn.config.properties.ViewDatabaseProperties;
+
+@Configuration
+@ConditionalOnProperty(value = "application.view-database.enabled", havingValue = "true")
+public class SecondaryStorageConfig {
+
+    @Bean
+    public DataSource dataSource(ViewDatabaseProperties viewDatabaseProperties) {
+        var databaseConfig = getHikariConfig(viewDatabaseProperties);
+        return new HikariDataSource(databaseConfig);
+    }
+
+    private HikariConfig getHikariConfig(ViewDatabaseProperties viewDatabaseProperties) {
+        var databaseConfig = new HikariConfig();
+        databaseConfig.setJdbcUrl(viewDatabaseProperties.getUrl());
+        databaseConfig.setUsername(viewDatabaseProperties.getUsername());
+        databaseConfig.setPassword(viewDatabaseProperties.getPassword());
+        databaseConfig.setAutoCommit(viewDatabaseProperties.isAutoCommitEnabled());
+        databaseConfig.setConnectionTimeout(viewDatabaseProperties.getConnectionTimeout());
+        databaseConfig.setMaximumPoolSize(viewDatabaseProperties.getMaxPoolSize());
+        return databaseConfig;
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/config/ServiceConfig.java

@@ -1,111 +1,56 @@
 package io.fairspace.saturn.config;
 
-import java.sql.SQLException;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import lombok.RequiredArgsConstructor;
-import org.keycloak.OAuth2Constants;
-import org.keycloak.admin.client.Keycloak;
-import org.keycloak.admin.client.KeycloakBuilder;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.apache.jena.query.Dataset;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.lang.Nullable;
 
-import io.fairspace.saturn.config.properties.CacheProperties;
-import io.fairspace.saturn.config.properties.FeatureProperties;
-import io.fairspace.saturn.config.properties.JenaProperties;
-import io.fairspace.saturn.config.properties.KeycloakClientProperties;
-import io.fairspace.saturn.config.properties.SearchProperties;
-import io.fairspace.saturn.config.properties.ViewDatabaseProperties;
-import io.fairspace.saturn.config.properties.WebDavProperties;
-import io.fairspace.saturn.rdf.SaturnDatasetFactory;
-import io.fairspace.saturn.services.IRIModule;
-import io.fairspace.saturn.services.users.UserService;
+import io.fairspace.saturn.config.properties.ViewsProperties;
+import io.fairspace.saturn.rdf.transactions.Transactions;
+import io.fairspace.saturn.services.search.FileSearchService;
+import io.fairspace.saturn.services.search.JdbcFileSearchService;
+import io.fairspace.saturn.services.search.SparqlFileSearchService;
+import io.fairspace.saturn.services.views.JdbcQueryService;
+import io.fairspace.saturn.services.views.QueryService;
 import io.fairspace.saturn.services.views.SparqlQueryService;
 import io.fairspace.saturn.services.views.ViewStoreClientFactory;
+import io.fairspace.saturn.services.views.ViewStoreReader;
+import io.fairspace.saturn.webdav.DavFactory;
 
-import static io.fairspace.saturn.config.ConfigLoader.VIEWS_CONFIG;
-
-import static com.fasterxml.jackson.databind.DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES;
-import static com.fasterxml.jackson.databind.SerializationFeature.WRITE_DATES_AS_TIMESTAMPS;
+import static io.fairspace.saturn.services.views.ViewStoreClientFactory.protectedResources;
 
-/**
- * Configuration for the Spark filter to enable the Saturn API.
- */
 @Configuration
-@RequiredArgsConstructor
 public class ServiceConfig {
 
-    // todo: make the init done by Spring
     @Bean
-    public Services getService(
-            Keycloak keycloak,
+    public QueryService queryService(
+            SparqlQueryService sparqlQueryService,
             @Nullable ViewStoreClientFactory viewStoreClientFactory,
-            FeatureProperties featureProperties,
-            JenaProperties jenaProperties,
-            CacheProperties cacheProperties,
-            SearchProperties searchProperties,
-            WebDavProperties webDavProperties,
-            KeycloakClientProperties keycloakClientProperties,
-            @Value("${application.publicUrl}") String publicUrl) {
-        var ds = SaturnDatasetFactory.connect(jenaProperties, viewStoreClientFactory, publicUrl);
-        return new Services(
-                VIEWS_CONFIG,
-                ds,
-                featureProperties,
-                viewStoreClientFactory,
-                keycloak.realm(keycloakClientProperties.getRealm()).users(),
-                jenaProperties,
-                cacheProperties,
-                searchProperties,
-                webDavProperties,
-                keycloakClientProperties,
-                publicUrl);
-    }
-
-    @Bean
-    @ConditionalOnProperty(value = "application.view-database.enabled", havingValue = "true")
-    public ViewStoreClientFactory getViewStoreClientFactory(
-            ViewDatabaseProperties viewDatabaseProperties, SearchProperties searchProperties) {
-        try {
-            return new ViewStoreClientFactory(VIEWS_CONFIG, viewDatabaseProperties, searchProperties);
-        } catch (SQLException e) {
-            throw new RuntimeException("Error connecting to the view database", e);
-        }
-    }
-
-    @Bean
-    public SparqlQueryService getSparqlQueryService(Services services) {
-        return services.getSparqlQueryService();
+            Transactions transactions,
+            @Qualifier("davFactory") DavFactory davFactory,
+            ViewStoreReader viewStoreReader) {
+        return viewStoreClientFactory == null
+                ? sparqlQueryService
+                : new JdbcQueryService(transactions, davFactory.root, viewStoreReader);
     }
 
     @Bean
-    public UserService getUserService(Services services) {
-        return services.getUserService();
-    }
-
-    @Bean
-    public Keycloak getKeycloak(KeycloakClientProperties keycloakClientProperties) {
-        return KeycloakBuilder.builder()
-                .serverUrl(keycloakClientProperties.getAuthServerUrl())
-                .realm(keycloakClientProperties.getRealm())
-                .grantType(OAuth2Constants.CLIENT_CREDENTIALS)
-                .clientId(keycloakClientProperties.getClientId())
-                .clientSecret(keycloakClientProperties.getClientSecret())
-                .username(keycloakClientProperties.getClientId())
-                .password(keycloakClientProperties.getClientSecret())
-                .build();
-    }
-
-    @Bean
-    public ObjectMapper objectMapper() {
-        return new ObjectMapper()
-                .registerModule(new IRIModule())
-                .registerModule(new JavaTimeModule())
-                .configure(WRITE_DATES_AS_TIMESTAMPS, false)
-                .configure(FAIL_ON_UNKNOWN_PROPERTIES, false);
+    public FileSearchService fileSearchService(
+            @Qualifier("filteredDataset") Dataset filteredDataset,
+            @Nullable ViewStoreClientFactory viewStoreClientFactory,
+            ViewsProperties viewsProperties,
+            Transactions transactions,
+            @Qualifier("davFactory") DavFactory davFactory,
+            ViewStoreReader viewStoreReader) {
+        // File search should be done using JDBC for performance reasons. However, if the view store is not available,
+        // or collections and files view is not configured, we fall back to using SPARQL queries on the RDF database
+        // directly.
+        boolean useSparqlFileSearchService = viewStoreClientFactory == null
+                || viewsProperties.views.stream().noneMatch(view -> protectedResources.containsAll(view.types));
+
+        return useSparqlFileSearchService
+                ? new SparqlFileSearchService(filteredDataset)
+                : new JdbcFileSearchService(transactions, davFactory.root, viewStoreReader);
     }
 }