Merge pull request #1567 from thehyve/refactoring/FAIRSPC-81

Refactoring/fairspc 81

projects/saturn/build.gradle

@@ -57,7 +57,6 @@ dependencies {
     implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${jacksonVersion}"
     implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${jacksonVersion}"
 
-    implementation "org.zoomba-lang:spark-core:3.0" // todo: to be replaced with Spring MVC
     implementation 'com.pivovarit:throwing-function:1.5.1'
     implementation 'com.google.guava:guava:33.0.0-jre'
     implementation('com.io-informatics.oss:jackson-jsonld:0.1.1') {
@@ -75,16 +74,13 @@ dependencies {
 
     testImplementation "junit:junit:4.13.2"
     testImplementation "org.mockito:mockito-core:${mockitoVersion}"
+    testImplementation 'org.springframework.boot:spring-boot-starter-test'
+    testImplementation 'org.junit.vintage:junit-vintage-engine:5.10.2'
     testImplementation "org.testcontainers:postgresql:1.19.6"
     testImplementation('com.github.stefanbirkner:system-rules:1.19.0') {
         exclude group: 'junit', module:'junit-dep'
     }
 
-    constraints {
-//        implementation('com.fasterxml.jackson.core:jackson-databind:2.9.10.1') {
-//            because 'previous versions have security vulnerabilities'
-//        }
-    }
 }
 
 jacocoTestReport {
@@ -117,4 +113,5 @@ test {
     // They also blocks usage of testing library mocking environment variables,
     // That is why this additional arg for tests is needed
     jvmArgs = ['--add-opens', 'java.base/java.util=ALL-UNNAMED']
+    useJUnitPlatform()
 }

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

@@ -2,6 +2,8 @@
 
 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;
@@ -20,12 +22,16 @@
 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.services.views.SparqlQueryService;
 import io.fairspace.saturn.services.views.ViewStoreClientFactory;
 
 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;
+
 /**
  * Configuration for the Spark filter to enable the Saturn API.
  */
@@ -93,4 +99,13 @@ public Keycloak getKeycloak(KeycloakClientProperties keycloakClientProperties) {
                 .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);
+    }
 }

projects/saturn/src/main/java/io/fairspace/saturn/controller/FeaturesController.java

@@ -0,0 +1,25 @@
+package io.fairspace.saturn.controller;
+
+import java.util.Set;
+
+import lombok.RequiredArgsConstructor;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import io.fairspace.saturn.config.Feature;
+import io.fairspace.saturn.config.properties.FeatureProperties;
+
+@RestController
+@RequestMapping("/features")
+@RequiredArgsConstructor
+public class FeaturesController {
+
+    private final FeatureProperties featureProperties;
+
+    @GetMapping("/")
+    public ResponseEntity<Set<Feature>> getFeatures() {
+        return ResponseEntity.ok(featureProperties.getFeatures());
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/controller/MaintenanceController.java

@@ -0,0 +1,36 @@
+package io.fairspace.saturn.controller;
+
+import lombok.RequiredArgsConstructor;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import io.fairspace.saturn.config.Services;
+
+@RestController
+@RequestMapping("/maintenance")
+@RequiredArgsConstructor
+public class MaintenanceController {
+
+    private final Services services;
+
+    @PostMapping("/reindex")
+    public ResponseEntity<Void> startReindex() {
+        services.getMaintenanceService().startRecreateIndexTask();
+        return ResponseEntity.noContent().build();
+    }
+
+    @PostMapping("/compact")
+    public ResponseEntity<Void> compactRdfStorage() {
+        services.getMaintenanceService().compactRdfStorageTask();
+        return ResponseEntity.noContent().build();
+    }
+
+    @GetMapping("/status")
+    public ResponseEntity<String> getStatus() {
+        var status = services.getMaintenanceService().active() ? "active" : "inactive";
+        return ResponseEntity.ok(status);
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/controller/MetadataController.java

@@ -0,0 +1,101 @@
+package io.fairspace.saturn.controller;
+
+import lombok.RequiredArgsConstructor;
+import lombok.extern.log4j.Log4j2;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.DeleteMapping;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PatchMapping;
+import org.springframework.web.bind.annotation.PutMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestHeader;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.ResponseStatus;
+import org.springframework.web.bind.annotation.RestController;
+
+import io.fairspace.saturn.config.Services;
+import io.fairspace.saturn.controller.validation.ValidIri;
+
+import static io.fairspace.saturn.controller.enums.CustomMediaType.APPLICATION_LD_JSON;
+import static io.fairspace.saturn.controller.enums.CustomMediaType.APPLICATION_N_TRIPLES;
+import static io.fairspace.saturn.controller.enums.CustomMediaType.TEXT_TURTLE;
+import static io.fairspace.saturn.services.metadata.Serialization.deserialize;
+import static io.fairspace.saturn.services.metadata.Serialization.getFormat;
+import static io.fairspace.saturn.services.metadata.Serialization.serialize;
+
+@Log4j2
+@RestController
+@RequestMapping("/metadata")
+@RequiredArgsConstructor
+@Validated
+public class MetadataController {
+
+    private static final String DO_VIEWS_UPDATE = "doViewsUpdate";
+
+    public static final String DO_VIEWS_UPDATE_DEFAULT_VALUE = "true";
+
+    private final Services services;
+
+    @GetMapping(
+            value = "/",
+            produces = {MediaType.APPLICATION_JSON_VALUE, APPLICATION_LD_JSON, TEXT_TURTLE, APPLICATION_N_TRIPLES})
+    public ResponseEntity<String> getMetadata(
+            @RequestParam(required = false) String subject,
+            @RequestParam(name = "withValueProperties", defaultValue = "false") boolean withValueProperties,
+            @RequestHeader(value = HttpHeaders.ACCEPT, required = false) String acceptHeader) {
+        var model = services.getMetadataService().get(subject, withValueProperties);
+        var format = getFormat(acceptHeader);
+        var metadata = serialize(model, format);
+        return ResponseEntity.ok(metadata);
+    }
+
+    @PutMapping(
+            value = "/",
+            consumes = {MediaType.APPLICATION_JSON_VALUE, APPLICATION_LD_JSON, TEXT_TURTLE, APPLICATION_N_TRIPLES})
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    public void putMetadata(
+            @RequestBody String body,
+            @RequestHeader(value = HttpHeaders.CONTENT_TYPE, required = false) String contentType,
+            @RequestParam(name = DO_VIEWS_UPDATE, defaultValue = DO_VIEWS_UPDATE_DEFAULT_VALUE)
+                    boolean doMaterializedViewsRefresh) {
+        Model model = deserialize(body, contentType);
+        services.getMetadataService().put(model, doMaterializedViewsRefresh);
+    }
+
+    @PatchMapping(
+            value = "/",
+            consumes = {MediaType.APPLICATION_JSON_VALUE, APPLICATION_LD_JSON, TEXT_TURTLE, APPLICATION_N_TRIPLES})
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    public void patchMetadata(
+            @RequestBody String body,
+            @RequestHeader(value = HttpHeaders.CONTENT_TYPE, required = false) String contentType,
+            @RequestParam(name = DO_VIEWS_UPDATE, defaultValue = DO_VIEWS_UPDATE_DEFAULT_VALUE) boolean doViewsUpdate) {
+        Model model = deserialize(body, contentType);
+        services.getMetadataService().patch(model, doViewsUpdate);
+    }
+
+    @DeleteMapping("/")
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    public void deleteMetadata(
+            @RequestParam(required = false) @ValidIri String subject,
+            @RequestBody(required = false) String body,
+            @RequestHeader(value = HttpHeaders.CONTENT_TYPE, required = false) String contentType,
+            @RequestParam(name = DO_VIEWS_UPDATE, defaultValue = DO_VIEWS_UPDATE_DEFAULT_VALUE)
+                    boolean doMaterializedViewsRefresh) {
+        if (subject != null) {
+            if (!services.getMetadataService().softDelete(ResourceFactory.createResource(subject))) {
+                throw new IllegalArgumentException("Subject could not be deleted");
+            }
+        } else {
+            Model model = deserialize(body, contentType);
+            services.getMetadataService().delete(model, doMaterializedViewsRefresh);
+        }
+    }
+}

projects/saturn/src/main/java/io/fairspace/saturn/controller/SearchController.java

@@ -0,0 +1,37 @@
+package io.fairspace.saturn.controller;
+
+import lombok.RequiredArgsConstructor;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import io.fairspace.saturn.config.Services;
+import io.fairspace.saturn.controller.dto.SearchResultsDto;
+import io.fairspace.saturn.controller.dto.request.FileSearchRequest;
+import io.fairspace.saturn.controller.dto.request.LookupSearchRequest;
+
+@RestController
+@RequestMapping("/search")
+@RequiredArgsConstructor
+public class SearchController {
+
+    private final Services services;
+
+    @PostMapping(value = "/files")
+    public ResponseEntity<SearchResultsDto> searchFiles(@RequestBody FileSearchRequest request) {
+        var searchResult = services.getFileSearchService().searchFiles(request);
+        var resultDto = SearchResultsDto.builder()
+                .results(searchResult)
+                .query(request.getQuery())
+                .build();
+        return ResponseEntity.ok(resultDto);
+    }
+
+    @PostMapping(value = "/lookup")
+    public ResponseEntity<SearchResultsDto> lookupSearch(@RequestBody LookupSearchRequest request) {
+        var results = services.getSearchService().getLookupSearchResults(request);
+        return ResponseEntity.ok(results);
+    }
+}