park changes.

agents/solr/pom.xml

@@ -12,11 +12,6 @@
 	</parent>
 
 	<dependencies>
-		<dependency>
-			<groupId>uk.ac.ebi.biosamples</groupId>
-			<artifactId>properties</artifactId>
-			<version>5.3.15-SNAPSHOT</version>
-		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>core</artifactId>

agents/solr/src/main/java/uk/ac/ebi/biosamples/solr/SolrRunner.java

@@ -16,9 +16,9 @@
 import org.springframework.boot.ApplicationArguments;
 import org.springframework.boot.ApplicationRunner;
 import org.springframework.stereotype.Component;
-import uk.ac.ebi.biosamples.BioSamplesProperties;
 import uk.ac.ebi.biosamples.messaging.MessagingConstants;
 import uk.ac.ebi.biosamples.messaging.service.MessageUtils;
+import uk.ac.ebi.biosamples.properties.BioSamplesProperties;
 
 @Component
 public class SolrRunner implements ApplicationRunner {

agents/uploadworkers/pom.xml

@@ -21,11 +21,6 @@
 			<artifactId>biosamples-spring-boot-starter</artifactId>
 			<version>5.3.15-SNAPSHOT</version>
 		</dependency>
-		<dependency>
-			<groupId>uk.ac.ebi.biosamples</groupId>
-			<artifactId>properties</artifactId>
-			<version>5.3.15-SNAPSHOT</version>
-		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.biosamples</groupId>
 			<artifactId>core</artifactId>

core/pom.xml

@@ -22,11 +22,6 @@
 	<dependencies>
 
 		<!-- === EBI dependencies === -->
-		<dependency>
-			<groupId>uk.ac.ebi.biosamples</groupId>
-			<artifactId>properties</artifactId>
-			<version>5.3.15-SNAPSHOT</version>
-		</dependency>
 		<dependency>
 			<groupId>uk.ac.ebi.ena.taxonomy</groupId>
 			<artifactId>sub-taxonomy-client</artifactId>

core/src/main/java/uk/ac/ebi/biosamples/advice/ModelAttributeControllerAdvice.java

@@ -13,7 +13,7 @@
 import java.net.URI;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.bind.annotation.ModelAttribute;
-import uk.ac.ebi.biosamples.BioSamplesProperties;
+import uk.ac.ebi.biosamples.properties.BioSamplesProperties;
 
 @ControllerAdvice
 public class ModelAttributeControllerAdvice {

webapps/core/src/main/java/uk/ac/ebi/biosamples/service/WebinAuthenticationService.java → core/src/main/java/uk/ac/ebi/biosamples/authentication/WebinAuthenticationService.java

@@ -8,25 +8,25 @@
 * CONDITIONS OF ANY KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations under the License.
 */
-package uk.ac.ebi.biosamples.service;
+package uk.ac.ebi.biosamples.authentication;
 
 import java.time.Instant;
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicBoolean;
 import org.springframework.stereotype.Service;
-import uk.ac.ebi.biosamples.BioSamplesProperties;
 import uk.ac.ebi.biosamples.core.model.CurationLink;
 import uk.ac.ebi.biosamples.core.model.Sample;
 import uk.ac.ebi.biosamples.core.model.SubmittedViaType;
 import uk.ac.ebi.biosamples.core.model.structured.AbstractData;
 import uk.ac.ebi.biosamples.core.model.structured.StructuredData;
 import uk.ac.ebi.biosamples.core.model.structured.StructuredDataType;
+import uk.ac.ebi.biosamples.core.service.SampleService;
 import uk.ac.ebi.biosamples.exception.GlobalExceptions;
+import uk.ac.ebi.biosamples.properties.BioSamplesProperties;
 import uk.ac.ebi.biosamples.security.service.BioSamplesCrossSourceIngestAccessControlService;
 
 @Service
 public class WebinAuthenticationService {
-  public static final String ATLANTICO_DOMAIN = "self.AtlantECO";
   private final SampleService sampleService;
   private final BioSamplesCrossSourceIngestAccessControlService
       bioSamplesCrossSourceIngestAccessControlService;

webapps/core-v2/src/main/java/uk/ac/ebi/biosamples/service/SampleService.java → core/src/main/java/uk/ac/ebi/biosamples/core/service/SampleService.java

@@ -8,10 +8,10 @@
 * CONDITIONS OF ANY KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations under the License.
 */
-package uk.ac.ebi.biosamples.service;
+package uk.ac.ebi.biosamples.core.service;
 
 import static java.util.stream.Collectors.toSet;
-import static uk.ac.ebi.biosamples.BioSamplesConstants.*;
+import static uk.ac.ebi.biosamples.properties.BioSamplesConstants.*;
 
 import java.time.Instant;
 import java.time.LocalDateTime;
@@ -25,20 +25,20 @@
 import org.springframework.security.core.Authentication;
 import org.springframework.security.core.userdetails.UserDetails;
 import org.springframework.stereotype.Service;
-import uk.ac.ebi.biosamples.BioSamplesProperties;
 import uk.ac.ebi.biosamples.core.model.Attribute;
 import uk.ac.ebi.biosamples.core.model.Relationship;
 import uk.ac.ebi.biosamples.core.model.Sample;
 import uk.ac.ebi.biosamples.core.model.SubmittedViaType;
 import uk.ac.ebi.biosamples.core.model.structured.AbstractData;
-import uk.ac.ebi.biosamples.core.service.SampleValidator;
 import uk.ac.ebi.biosamples.exception.GlobalExceptions;
 import uk.ac.ebi.biosamples.mongo.model.MongoSample;
 import uk.ac.ebi.biosamples.mongo.model.MongoSampleMessage;
 import uk.ac.ebi.biosamples.mongo.repository.MongoSampleMessageRepository;
 import uk.ac.ebi.biosamples.mongo.repository.MongoSampleRepository;
 import uk.ac.ebi.biosamples.mongo.service.*;
+import uk.ac.ebi.biosamples.properties.BioSamplesProperties;
 import uk.ac.ebi.biosamples.security.service.BioSamplesCrossSourceIngestAccessControlService;
+import uk.ac.ebi.biosamples.service.MessagingService;
 
 /**
  * Service layer business logic for centralizing repository access and conversions between different

core/src/main/java/uk/ac/ebi/biosamples/mongo/service/MongoAccessionService.java

@@ -21,15 +21,17 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.data.mongodb.core.MongoOperations;
 import org.springframework.data.mongodb.core.query.Update;
-import uk.ac.ebi.biosamples.BioSamplesConstants;
+import org.springframework.stereotype.Service;
 import uk.ac.ebi.biosamples.core.model.Attribute;
 import uk.ac.ebi.biosamples.core.model.Sample;
 import uk.ac.ebi.biosamples.mongo.model.MongoRelationship;
 import uk.ac.ebi.biosamples.mongo.model.MongoSample;
 import uk.ac.ebi.biosamples.mongo.model.MongoSequence;
 import uk.ac.ebi.biosamples.mongo.repository.MongoSampleRepository;
+import uk.ac.ebi.biosamples.properties.BioSamplesConstants;
 
 // this needs to be the spring exception, not the mongo one
+@Service("SampleAccessionService")
 public class MongoAccessionService {
   private final Logger log = LoggerFactory.getLogger(getClass());
   private final MongoSampleRepository mongoSampleRepository;

core/src/main/java/uk/ac/ebi/biosamples/mongo/service/SampleReadService.java

@@ -20,14 +20,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Service;
-import uk.ac.ebi.biosamples.BioSamplesConstants;
-import uk.ac.ebi.biosamples.BioSamplesProperties;
 import uk.ac.ebi.biosamples.core.model.Sample;
 import uk.ac.ebi.biosamples.core.model.structured.StructuredData;
 import uk.ac.ebi.biosamples.mongo.model.MongoSample;
 import uk.ac.ebi.biosamples.mongo.model.MongoStructuredData;
 import uk.ac.ebi.biosamples.mongo.repository.MongoSampleRepository;
 import uk.ac.ebi.biosamples.mongo.repository.MongoStructuredDataRepository;
+import uk.ac.ebi.biosamples.properties.BioSamplesConstants;
+import uk.ac.ebi.biosamples.properties.BioSamplesProperties;
 import uk.ac.ebi.biosamples.utils.thread.AdaptiveThreadPoolExecutor;
 
 /**

properties/src/main/java/uk/ac/ebi/biosamples/BioSamplesConstants.java → core/src/main/java/uk/ac/ebi/biosamples/properties/BioSamplesConstants.java

@@ -8,7 +8,7 @@
 * CONDITIONS OF ANY KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations under the License.
 */
-package uk.ac.ebi.biosamples;
+package uk.ac.ebi.biosamples.properties;
 
 import java.util.Set;