Sample status tracking in BioSamples

.gitlab-ci.yml

@@ -35,8 +35,6 @@ maven-package-all-apps:
       - agents/uploadworkers/target/agents-uploadworkers-*.jar
       - pipelines/reindex/target/pipelines-reindex-*.jar
       - pipelines/curation/target/pipelines-curation-*.jar
-      - pipelines/curami/target/pipelines-curami-*.jar
-      - pipelines/copydown/target/pipelines-copydown-*.jar
 
 build_and_push_docker_images:
   stage: package
@@ -57,10 +55,6 @@ build_and_push_docker_images:
         DOCKERFILE_TARGET: "pipelines-reindex"
       - APP_NAME: "pipelines-curation"
         DOCKERFILE_TARGET: "pipelines-curation"
-      - APP_NAME: "pipelines-curami"
-        DOCKERFILE_TARGET: "pipelines-curami"
-      - APP_NAME: "pipelines-copydown"
-        DOCKERFILE_TARGET: "pipelines-copydown"
   script:
     - |
       DOCKER_IMAGE_NAME="$CI_REGISTRY_IMAGE/$APP_NAME:$DOCKER_TAG"
@@ -87,6 +81,7 @@ clone-config:
       - config
   only:
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search
@@ -100,6 +95,7 @@ deploy_k8s_primary_dev:
     url: https://wwwdev.ebi.ac.uk/biosamples
   only:
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search
@@ -115,6 +111,7 @@ deploy_k8s_primary_prod:
     url: https://www.ebi.ac.uk/biosamples
   only:
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search
@@ -130,6 +127,7 @@ deploy_k8s_fallback_prod:
     url: https://www.ebi.ac.uk/biosamples
   only:
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search
@@ -145,6 +143,7 @@ deploy_pipeline_k8s_primary_prod:
     url: https://www.ebi.ac.uk/biosamples
   only: 
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search
@@ -160,6 +159,7 @@ deploy_pipeline_k8s_fallback_prod:
     url: https://www.ebi.ac.uk/biosamples
   only:
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search
@@ -175,6 +175,7 @@ deploy_pipeline_k8s_primary_dev:
     url: https://wwwdev.ebi.ac.uk/biosamples
   only:
     - chore/working-es-search-k8-deployment-with-cleanup
+    - chore/BSD-2547-sample-status-management
     - dev
     - main
     - biosamples-search

client/client/src/main/java/uk/ac/ebi/biosamples/client/BioSamplesClient.java

@@ -20,7 +20,6 @@
 import org.springframework.boot.web.client.RestTemplateBuilder;
 import org.springframework.hateoas.EntityModel;
 import org.springframework.hateoas.MediaTypes;
-import org.springframework.hateoas.PagedModel;
 import org.springframework.hateoas.client.Traverson;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpRequest;
@@ -46,7 +45,6 @@ public class BioSamplesClient implements AutoCloseable {
   private final Logger log = LoggerFactory.getLogger(getClass());
   private final SampleRetrievalService sampleRetrievalService;
   private final SampleRetrievalServiceV2 sampleRetrievalServiceV2;
-  private final SamplePageRetrievalService samplePageRetrievalService;
   private final SampleCursorRetrievalService sampleCursorRetrievalService;
   private final SampleSubmissionService sampleSubmissionService;
   private final SampleSubmissionServiceV2 sampleSubmissionServiceV2;
@@ -98,7 +96,6 @@ public BioSamplesClient(
     traverson.setRestOperations(restOperations);
 
     sampleRetrievalService = new SampleRetrievalService(restOperations, traverson);
-    samplePageRetrievalService = new SamplePageRetrievalService(restOperations, traverson);
     sampleCursorRetrievalService = new SampleCursorRetrievalService(restOperations, traverson);
     sampleSubmissionService = new SampleSubmissionService(restOperations, traverson);
     sampleSubmissionServiceV2 = new SampleSubmissionServiceV2(restOperations, uriV2);
@@ -335,36 +332,6 @@ public Iterable<Optional<EntityModel<Sample>>> fetchSampleResourceAll(
     return sampleRetrievalService.fetchAll(accessions);
   }
 
-  /**
-   * Searches for samples using pagination. This method should be used for specific pagination
-   * needs. When in need for all results from a search, prefer the iterator implementation.
-   *
-   * @param text the text query
-   * @param page the page number
-   * @param size the page size
-   * @return a paged model of sample resources
-   */
-  public PagedModel<EntityModel<Sample>> fetchPagedSampleResource(
-      final String text, final int page, final int size) {
-    return samplePageRetrievalService.search(text, Collections.emptyList(), page, size);
-  }
-
-  /**
-   * Searches for samples using pagination with specified filters. This method should be used for
-   * specific pagination needs. When in need for all results from a search, prefer the iterator
-   * implementation.
-   *
-   * @param text the text query
-   * @param filters the collection of filters
-   * @param page the page number
-   * @param size the page size
-   * @return a paged model of sample resources
-   */
-  public PagedModel<EntityModel<Sample>> fetchPagedSampleResource(
-      final String text, final Collection<Filter> filters, final int page, final int size) {
-    return samplePageRetrievalService.search(text, filters, page, size);
-  }
-
   /**
    * Deprecated method: Persists a sample using BioSamples.
    *
@@ -510,15 +477,6 @@ public Iterable<EntityModel<Sample>> fetchSampleResourceAll(
     return sampleCursorRetrievalService.fetchAll(text, filters, jwt);
   }
 
-  public PagedModel<EntityModel<Sample>> fetchPagedSampleResource(
-      final String text,
-      final Collection<Filter> filters,
-      final int page,
-      final int size,
-      final String jwt) {
-    return samplePageRetrievalService.search(text, filters, page, size, jwt);
-  }
-
   public EntityModel<Sample> persistSampleResource(final Sample sample, final String jwt) {
     final Collection<String> errors = sampleValidator.validate(sample);
 

client/client/src/main/java/uk/ac/ebi/biosamples/client/service/SampleCursorRetrievalService.java

@@ -70,7 +70,6 @@ public Iterable<EntityModel<Sample>> fetchAll(
     }
 
     params.add("applyCurations", String.valueOf(addCurations));
-
     params = encodePlusInQueryParameters(params);
 
     return new IterableResourceFetchAll<>(

client/client/src/main/java/uk/ac/ebi/biosamples/client/utils/IterableResourceFetchAll.java

@@ -38,6 +38,28 @@
 import org.springframework.web.util.UriComponentsBuilder;
 import org.springframework.web.util.UriTemplate;
 
+/**
+ * Provides an {@link Iterable} view over a paginated HAL resource and transparently fetches
+ * additional pages as iteration progresses.
+ *
+ * <p>This utility is intended for clients that need to consume a collection of {@link EntityModel}
+ * instances without manually handling pagination. It starts from the initial page discovered
+ * through {@link Traverson}, then iterates through all available pages by requesting later page
+ * links on demand. The implementation is designed to hide the paging mechanics from callers so that
+ * the result can be processed with a standard Java-enhanced for-loop or any other {@link
+ * Iterable}-based API.
+ *
+ * <p>When iterating, the current page is consumed first. If another page is available, the next
+ * page request is prepared and executed asynchronously using the supplied {@link ExecutorService}.
+ * This allows the next page to be fetched while the current page is still being processed, which
+ * can reduce waiting time for large result sets. Authentication information may be propagated via
+ * the optional JWT value when performing page requests.
+ *
+ * <p>The class also supports applying query parameters to the initial traversal, making it useful
+ * for fetching filtered result sets from REST endpoints that expose paginated representations.
+ *
+ * @param <T> the resource type contained in each {@link EntityModel}
+ */
 @Slf4j
 public class IterableResourceFetchAll<T> implements Iterable<EntityModel<T>> {
   private final Traverson traverson;
@@ -117,6 +139,9 @@ public Iterator<EntityModel<T>> iterator() {
 
     // Build the URI with encoding disabled to preserve existing encoding
     final URI finalUri = uriBuilder.build(false).toUri();
+
+    log.info("First Uri {}", finalUri);
+
     final RequestEntity<Void> requestEntity =
         IteratorResourceFetchAll.NextPageCallable.buildRequestEntity(jwt, finalUri);
     final ResponseEntity<PagedModel<EntityModel<T>>> responseEntity =
@@ -187,7 +212,7 @@ public synchronized boolean hasNext() {
                 .build(true)
                 .toUri();
 
-        log.trace("Getting next page uri " + uri);
+        log.info("Next page uri " + uri);
 
         nextPageFuture =
             executor.submit(

core/src/main/java/uk/ac/ebi/biosamples/core/model/Sample.java

@@ -544,7 +544,7 @@ public static Sample build(
 
     sample.reviewed = reviewed;
 
-    // Validation moved to a later stage, to capture the error (SampleService.store())
+    // Validation moved to a later stage to capture the error (SampleService.store())
     sample.release = release;
 
     if (status != null) {

core/src/main/java/uk/ac/ebi/biosamples/core/model/SampleStatus.java

@@ -19,7 +19,9 @@ public enum SampleStatus {
   PUBLIC,
   CANCELLED,
   SUPPRESSED,
-  KILLED;
+  KILLED,
+  TEMPORARY_SUPPRESSED,
+  TEMPORARY_KILLED;
 
   public static List<String> getSearchHiddenStatuses() {
     return Arrays.asList(SUPPRESSED.name(), KILLED.name());