From fd741c96be80477f84aabbdd0fc1edd21f7c3ece Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Tue, 3 Jun 2025 18:07:38 +0200
Subject: [PATCH 01/11] feat: index datasetCount of dataverses

---
 conf/solr/schema.xml                          |  1 +
 .../iq/dataverse/DatasetServiceBean.java      |  2 +-
 .../iq/dataverse/DataverseServiceBean.java    | 30 ++++++++++++++++---
 .../command/impl/LinkDatasetCommand.java      | 10 +++++++
 .../iq/dataverse/search/IndexServiceBean.java |  9 ++++++
 .../iq/dataverse/search/SearchFields.java     |  1 +
 .../dataverse/search/SearchServiceBean.java   |  2 ++
 .../iq/dataverse/search/SolrSearchResult.java | 13 ++++++++
 8 files changed, 63 insertions(+), 5 deletions(-)

diff --git a/conf/solr/schema.xml b/conf/solr/schema.xml
index 50835957b04..4d87f59df91 100644
--- a/conf/solr/schema.xml
+++ b/conf/solr/schema.xml
@@ -241,6 +241,7 @@
 
     <field name="license" type="string" stored="true" indexed="true" multiValued="false"/>
     <field name="fileCount" type="plong" stored="true" indexed="true" multiValued="false"/>
+    <field name="datasetCount" type="plong" stored="true" indexed="true" multiValued="false"/>
     
     <!--
         METADATA SCHEMA FIELDS
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
index 202800d027b..b4c57e44bd3 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -168,7 +168,7 @@ public List<Long> findIdsByOwnerId(Long ownerId) {
         return findIdsByOwnerId(ownerId, false);
     }
 
-    private List<Long> findIdsByOwnerId(Long ownerId, boolean onlyPublished) {
+    public List<Long> findIdsByOwnerId(Long ownerId, boolean onlyPublished) {
         List<Long> retList = new ArrayList<>();
         if (!onlyPublished) {
             return em.createNamedQuery("Dataset.findIdByOwnerId")
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
index f89e707cc03..b7d9c964b60 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
@@ -468,8 +468,26 @@ public List<Dataverse> findDataversesThatLinkToThisDvId(long dataverseId) {
         return dataverseLinkingService.findLinkingDataverses(dataverseId);
     }
 
+    public List<Dataset> findDatasetsThisIdHasLinkedTo(long dataverseId, boolean onlyPublished) {
+        List<Dataset> linkedDatasets = datasetLinkingService.findLinkedDatasets(dataverseId);
+
+        if (!onlyPublished) {
+            return linkedDatasets;
+        }
+
+        List<Dataset> retList = new ArrayList();
+
+        for (Dataset ds : linkedDatasets) {
+            if (ds.isReleased() && !ds.isDeaccessioned()) {
+                retList.add(ds);
+            }
+        }
+
+        return retList;
+    }
+
     public List<Dataset> findDatasetsThisIdHasLinkedTo(long dataverseId) {
-        return datasetLinkingService.findLinkedDatasets(dataverseId);
+        return this.findDatasetsThisIdHasLinkedTo(dataverseId, false);
     }
 
     public List<Dataverse> findDataversesThatLinkToThisDatasetId(long datasetId) {
@@ -754,21 +772,25 @@ public List<Long> findAllDataverseDataverseChildren(Long dvId) {
     
     // function to recursively find ids of all children of a dataverse that are 
     // of type dataset
-    public List<Long> findAllDataverseDatasetChildren(Long dvId) {
+    public List<Long> findAllDataverseDatasetChildren(Long dvId, boolean onlyPublished) {
         // get list of Dataverse children
         List<Long> dataverseChildren = findIdsByOwnerId(dvId);
         // get list of Dataset children
-        List<Long> datasetChildren = datasetService.findIdsByOwnerId(dvId);
+        List<Long> datasetChildren = datasetService.findIdsByOwnerId(dvId, onlyPublished);
         
         if (dataverseChildren == null) {
             return datasetChildren;
         } else {
             for (Long childDvId : dataverseChildren) {
-                datasetChildren.addAll(findAllDataverseDatasetChildren(childDvId));
+                datasetChildren.addAll(findAllDataverseDatasetChildren(childDvId, onlyPublished));
             }
             return datasetChildren;
         }
     }
+
+    public List<Long> findAllDataverseDatasetChildren(Long dvId) {
+        return findAllDataverseDatasetChildren(dvId, false);
+    }
     
     public String addRoleAssignmentsToChildren(Dataverse owner, ArrayList<String> rolesToInherit,
             boolean inheritAllRoles) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java
index aef749d7e26..54630f3e64e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java
@@ -71,6 +71,16 @@ public boolean onSuccess(CommandContext ctxt, Object r) {
 
         ctxt.index().asyncIndexDataset(dld.getDataset(), true);
 
+        Dataverse linkingDataverse = dld.getLinkingDataverse();
+        try {
+            ctxt.index().indexDataverse(linkingDataverse);
+        } catch (IOException | SolrServerException e) {
+            String failureLogText = "Indexing of linking dataverse failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + linkingDataverse.getId().toString();
+            failureLogText += "\r\n" + e.getLocalizedMessage();
+            LoggingUtil.writeOnSuccessFailureLog(null, failureLogText, linkingDataverse);
+            return false;
+        }
+
         return retVal;
     }
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
index a38a8679209..4d50958da51 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
@@ -315,6 +315,15 @@ public Future<String> indexDataverse(Dataverse dataverse, boolean processPaths)
         }
         
         solrInputDocument.addField(SearchFields.SUBTREE, dataversePaths);
+
+        if (dataverse.isReleased()) {
+            // Get all datasets published in this dataverse, including harvested datasets
+            int numberOfPublishedDatasets = dataverseService.findAllDataverseDatasetChildren(dataverse.getId(), true).size();
+            // Get all published datasets linked to this dataverse
+            int numberOfLinkedDatasets = dataverseService.findDatasetsThisIdHasLinkedTo(dataverse.getId(), true).size();
+            solrInputDocument.addField(SearchFields.DATASET_COUNT, numberOfPublishedDatasets + numberOfLinkedDatasets);
+        }
+
         docs.add(solrInputDocument);
 
         String status;
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java
index 109c17d6ef9..0d65a03c853 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchFields.java
@@ -296,5 +296,6 @@ more targeted results for just datasets. The format is YYYY (i.e.
 
     public static final String DATASET_LICENSE = "license";
     public static final String FILE_COUNT = "fileCount";
+    public static final String DATASET_COUNT = "datasetCount";
 
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java
index 08ddbab202a..ca192b43572 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SearchServiceBean.java
@@ -506,6 +506,7 @@ public SolrQueryResponse search(
             //
             Boolean datasetValid = (Boolean) solrDocument.getFieldValue(SearchFields.DATASET_VALID);
             Long fileCount = (Long) solrDocument.getFieldValue(SearchFields.FILE_COUNT);
+            Long datasetCount = (Long) solrDocument.getFieldValue(SearchFields.DATASET_COUNT);
             
             List<String> matchedFields = new ArrayList<>();
             
@@ -580,6 +581,7 @@ public SolrQueryResponse search(
             solrSearchResult.setDvTree(dvTree);
             solrSearchResult.setDatasetValid(datasetValid);
             solrSearchResult.setFileCount(fileCount);
+            solrSearchResult.setDatasetCount(datasetCount);
 
             if (Boolean.TRUE.equals((Boolean) solrDocument.getFieldValue(SearchFields.IS_HARVESTED))) {
                 solrSearchResult.setHarvested(true);
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
index c34743532bd..e187eeab899 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/SolrSearchResult.java
@@ -82,6 +82,10 @@ public class SolrSearchResult {
     * Only Dataset can have a file count
     */
     private Long fileCount;
+    /**
+     * Only Dataverses can have a dataset count
+     */
+    private Long datasetCount;
     /**
      * Files and datasets might have a UNF. Dataverses don't.
      */
@@ -702,6 +706,7 @@ public JsonObjectBuilder json(boolean showRelevance, boolean showEntityIds, bool
                 nullSafeJsonBuilder.add("affiliation", dataverseAffiliation);
                 nullSafeJsonBuilder.add("parentDataverseName", dataverseParentName);
                 nullSafeJsonBuilder.add("parentDataverseIdentifier", dataverseParentAlias);
+                nullSafeJsonBuilder.add("datasetCount", this.datasetCount);
             } else if (this.entity.isInstanceofDataFile()) {
                 // "published_at" field is only set when the version state is not draft.
                 // On the contrary, this field also takes into account DataFiles in draft version,
@@ -1402,4 +1407,12 @@ public Long getFileCount() {
     public void setFileCount(Long fileCount) {
         this.fileCount = fileCount;
     }
+
+    public Long getDatasetCount() {
+        return datasetCount;
+    }
+
+    public void setDatasetCount(Long datasetCount) {
+        this.datasetCount = datasetCount;
+    }
 }

From e30d21425d6840bafe9bf74a26eacfa0c0298cb9 Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Wed, 4 Jun 2025 16:06:24 +0200
Subject: [PATCH 02/11] test: add test for filtering + retrieving datasetCount
 of dataverses using search API

---
 .../harvard/iq/dataverse/api/SearchIT.java    | 194 ++++++++++++++++++
 1 file changed, 194 insertions(+)

diff --git a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
index 37e8b30a9f5..44d033711ec 100644
--- a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
+++ b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
@@ -31,6 +31,7 @@
 
 import jakarta.json.JsonObjectBuilder;
 
+import static io.restassured.RestAssured.given;
 import static jakarta.ws.rs.core.Response.Status.*;
 import static java.lang.Thread.sleep;
 import java.nio.file.Path;
@@ -41,6 +42,7 @@
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 
 public class SearchIT {
 
@@ -1628,6 +1630,198 @@ public void testSearchWithInvalidDateField() {
 
     }
 
+    @Test
+    public void testDataverseDatasetCounts() throws InterruptedException {
+        Response createUser = UtilIT.createRandomUser();
+        createUser.prettyPrint();
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+        Response makeSuperuser = UtilIT.makeSuperUser(username);
+        makeSuperuser.prettyPrint();
+        makeSuperuser.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        Response createDataverseResponse = UtilIT.createRandomDataverse(apiToken);
+        createDataverseResponse.prettyPrint();
+        String dataverseAlias = UtilIT.getAliasFromResponse(createDataverseResponse);
+
+        Response publishDataverse = UtilIT.publishDataverseViaNativeApi(dataverseAlias, apiToken);
+        publishDataverse.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Wait for reindex of dataverse after publishing
+        String searchEmptyDataverseQuery = "identifier:" + dataverseAlias + " AND publicationStatus:Published AND datasetCount:0";
+        assertTrue(UtilIT.sleepForSearch(searchEmptyDataverseQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchEmptyDataverse = UtilIT.search(searchEmptyDataverseQuery, apiToken, "&type=dataverse");
+        searchEmptyDataverse.prettyPrint();
+        searchEmptyDataverse.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
+
+        // Check that published datasets are counted
+        Response createDatasetResponse = UtilIT.createRandomDatasetViaNativeApi(dataverseAlias, apiToken);
+        createDatasetResponse.prettyPrint();
+        Integer datasetId = UtilIT.getDatasetIdFromResponse(createDatasetResponse);
+        String datasetPid = JsonPath.from(createDatasetResponse.getBody().asString()).getString("data.persistentId");
+
+        Response publishDataset = UtilIT.publishDatasetViaNativeApi(datasetPid, "major", apiToken);
+        publishDataset.then().assertThat()
+                .statusCode(OK.getStatusCode());
+        UtilIT.sleepForReindex(datasetPid, apiToken, 5);
+
+        // Wait for reindex of dataverse after publishing
+        String searchDataverseWithDatasetQuery = "identifier:" + dataverseAlias + " AND datasetCount:1";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithDatasetQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithDataset = UtilIT.search(searchDataverseWithDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithDataset.prettyPrint();
+        searchDataverseWithDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(1));
+
+        Response createDataverseResponse2 = UtilIT.createRandomDataverse(apiToken);
+        createDataverseResponse2.prettyPrint();
+        String dataverseAlias2 = UtilIT.getAliasFromResponse(createDataverseResponse2);
+
+        Response publishDataverse2 = UtilIT.publishDataverseViaNativeApi(dataverseAlias2, apiToken);
+        publishDataverse2.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Wait for reindex of dataverse after publishing
+        String searchEmptyDataverse2Query = "identifier:" + dataverseAlias2 + " AND publicationStatus:Published AND datasetCount:0";
+        assertTrue(UtilIT.sleepForSearch(searchEmptyDataverse2Query, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchEmptyDataverse2 = UtilIT.search(searchEmptyDataverse2Query, apiToken, "&type=dataverse");
+        searchEmptyDataverse2.prettyPrint();
+        searchEmptyDataverse2.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias2))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
+
+        // Check that linked datasets are counted
+        Response linkDataset = UtilIT.linkDataset(datasetPid, dataverseAlias2, apiToken);
+        linkDataset.prettyPrint();
+        linkDataset.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Wait for reindex of dataverse after linking
+        String searchDataverseWithLinkedDatasetQuery = "identifier:" + dataverseAlias2 + " AND datasetCount:1";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithLinkedDatasetQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithLinkedDataset = UtilIT.search(searchDataverseWithLinkedDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithLinkedDataset.prettyPrint();
+        searchDataverseWithLinkedDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias2))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(1));
+
+        // Check that harvested datasets are counted
+        // TODO Harvesting fails with "lastResult": "Completed with failures",
+//        Response createDataverseResponse3 = UtilIT.createRandomDataverse(apiToken);
+//        createDataverseResponse3.prettyPrint();
+//        String dataverseAlias3 = UtilIT.getAliasFromResponse(createDataverseResponse3);
+//
+//        Response publishDataverse3 = UtilIT.publishDataverseViaNativeApi(dataverseAlias3, apiToken);
+//        publishDataverse3.then().assertThat()
+//                .statusCode(OK.getStatusCode());
+//
+//        String nickName = "h" + UtilIT.getRandomString(6);
+//        String sourceName = "";
+//
+//        String clientApiPath = String.format("/api/harvest/clients/%s", nickName);
+//        String clientJson = String.format("{\"dataverseAlias\":\"%s\","
+//                        + "\"type\":\"oai\","
+//                        + "\"sourceName\":\"%s\","
+//                        + "\"harvestUrl\":\"%s\","
+//                        + "\"archiveUrl\":\"%s\","
+//                        + "\"set\":\"%s\","
+//                        + "\"allowHarvestingMissingCVV\":%s,"
+//                        + "\"metadataFormat\":\"%s\"}",
+//                dataverseAlias3, sourceName, "https://demo.dataverse.org/oai", "https://demo.dataverse.org",
+//                "controlTestSet2", false, "oai_dc");
+//
+//        Response createResponse = given()
+//                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
+//                .body(clientJson)
+//                .post(clientApiPath);
+//        createResponse.prettyPrint();
+//        assertEquals(CREATED.getStatusCode(), createResponse.getStatusCode());
+//
+//        String runHarvestApiPath = String.format("/api/harvest/clients/%s/run", nickName);
+//
+//        Response runResponse = given()
+//                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
+//                .post(runHarvestApiPath);
+//        runResponse.prettyPrint();
+//        assertEquals(ACCEPTED.getStatusCode(), runResponse.getStatusCode());
+//
+//        int i = 0;
+//        int maxWait=20; // a very conservative interval; this harvest has no business taking this long
+//        int numberOfDatasetsHarvested = 0;
+//        do {
+//            // Give it an initial 2 sec. delay, to make sure the client state
+//            // has been updated in the database, which can take some appreciable
+//            // amount of time on a heavily-loaded server running a full suite of
+//            // tests:
+//            Thread.sleep(2000L);
+//            // keep checking the status of the client with the GET api:
+//            Response getClientResponse = given()
+//                    .get(clientApiPath);
+//
+//            assertEquals(OK.getStatusCode(), getClientResponse.getStatusCode());
+//            JsonPath responseJsonPath = getClientResponse.body().jsonPath();
+//            assertNotNull(responseJsonPath, "Invalid JSON in GET client response");
+//            assertEquals(ApiConstants.STATUS_OK, responseJsonPath.getString("status"));
+//
+//            String clientStatus = responseJsonPath.getString("data.status");
+//            assertNotNull(clientStatus);
+//
+//            if ("inProgress".equals(clientStatus) || "IN PROGRESS".equals(responseJsonPath.getString("data.lastResult"))) {
+//                // we'll sleep for 2 more seconds
+//                i++;
+//            } else {
+//                logger.info("getClientResponse.prettyPrint: "
+//                        + getClientResponse.prettyPrint());
+//                // Check the values in the response:
+//                // a) Confirm that the harvest has completed:
+//                assertEquals("inActive", clientStatus, "Unexpected client status: "+clientStatus);
+//
+//                // b) Confirm that it has actually succeeded:
+//                assertTrue(responseJsonPath.getString("data.lastResult").contains("Completed"), "Last harvest not reported a success (took "+i+" seconds)");
+//                String harvestTimeStamp = responseJsonPath.getString("data.lastHarvest");
+//                assertNotNull(harvestTimeStamp);
+//
+//                // c) Confirm that at least one dataset has been harvested:
+//                numberOfDatasetsHarvested = responseJsonPath.getInt("data.lastDatasetsHarvested");
+//                assertTrue(numberOfDatasetsHarvested > 0);
+//
+//                // ok, it looks like the harvest has completed successfully.
+//                break;
+//            }
+//        } while (i<maxWait);
+//
+//        System.out.println("Waited " + i + " seconds for the harvest to complete.");
+//
+//        // Wait for reindex of dataverse after harvesting
+//        String searchDataverseWithHarvestedDatasetQuery = "identifier:" + dataverseAlias3 + " AND datasetCount:" + numberOfDatasetsHarvested;
+//        assertTrue(UtilIT.sleepForSearch(searchDataverseWithHarvestedDatasetQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+//
+//        Response searchDataverseWithHarvestedDataset = UtilIT.search(searchDataverseWithHarvestedDatasetQuery, apiToken, "&type=dataverse");
+//        searchDataverseWithHarvestedDataset.prettyPrint();
+//        searchDataverseWithHarvestedDataset.then().assertThat()
+//                .statusCode(OK.getStatusCode())
+//                .body("data.total_count", CoreMatchers.equalTo(1))
+//                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias3))
+//                .body("data.items[0].datasetCount", CoreMatchers.equalTo(numberOfDatasetsHarvested));
+    }
+
     @AfterEach
     public void tearDownDataverse() {
         File treesThumb = new File("scripts/search/data/binary/trees.png.thumb48");

From dc8d6800fb51ac19435d71f576fd37c6d798e1b6 Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Wed, 4 Jun 2025 16:23:06 +0200
Subject: [PATCH 03/11] docs: add release note for datasetCount

---
 doc/release-notes/10190-dataset-count.md | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 doc/release-notes/10190-dataset-count.md

diff --git a/doc/release-notes/10190-dataset-count.md b/doc/release-notes/10190-dataset-count.md
new file mode 100644
index 00000000000..5da89edcdb6
--- /dev/null
+++ b/doc/release-notes/10190-dataset-count.md
@@ -0,0 +1,2 @@
+The search index now includes datasetCount for each collection, counting both published and linked datasets.
+Collections can be filtered using datasetCount (e.g., `datasetCount:[1000 TO *]`), and the value is returned in Dataverse search results via the Search API.
\ No newline at end of file

From b5f2580f3eaaa4c6e92297438fd9cb6ebe1bf830 Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Thu, 5 Jun 2025 12:48:23 +0200
Subject: [PATCH 04/11] feat: include harvested datasets in datasetCount

---
 .../iq/dataverse/DatasetServiceBean.java      |  10 +-
 .../iq/dataverse/DataverseServiceBean.java    |   8 +-
 .../harvest/client/HarvesterServiceBean.java  |   7 +
 .../client/HarvestingClientServiceBean.java   |  11 +
 .../iq/dataverse/search/IndexServiceBean.java |   2 +-
 .../harvard/iq/dataverse/api/SearchIT.java    | 218 ++++++++++--------
 6 files changed, 146 insertions(+), 110 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
index b4c57e44bd3..cb726b2ccd8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -165,12 +165,12 @@ private List<Dataset> findByOwnerId(Long ownerId, boolean onlyPublished) {
     }
 
     public List<Long> findIdsByOwnerId(Long ownerId) {
-        return findIdsByOwnerId(ownerId, false);
+        return findIdsByOwnerId(ownerId, false, false);
     }
 
-    public List<Long> findIdsByOwnerId(Long ownerId, boolean onlyPublished) {
+    public List<Long> findIdsByOwnerId(Long ownerId, boolean onlyPublished, boolean includeHarvested) {
         List<Long> retList = new ArrayList<>();
-        if (!onlyPublished) {
+        if (!onlyPublished && includeHarvested) {
             return em.createNamedQuery("Dataset.findIdByOwnerId")
                     .setParameter("ownerId", ownerId)
                     .getResultList();
@@ -178,7 +178,9 @@ public List<Long> findIdsByOwnerId(Long ownerId, boolean onlyPublished) {
             List<Dataset> results = em.createNamedQuery("Dataset.findByOwnerId")
                     .setParameter("ownerId", ownerId).getResultList();
             for (Dataset ds : results) {
-                if (ds.isReleased() && !ds.isDeaccessioned()) {
+                if (onlyPublished && ds.isReleased() && !ds.isDeaccessioned()) {
+                    retList.add(ds.getId());
+                } else if (includeHarvested && ds.isHarvested()) {
                     retList.add(ds.getId());
                 }
             }
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
index b7d9c964b60..91d4e861e15 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
@@ -772,24 +772,24 @@ public List<Long> findAllDataverseDataverseChildren(Long dvId) {
     
     // function to recursively find ids of all children of a dataverse that are 
     // of type dataset
-    public List<Long> findAllDataverseDatasetChildren(Long dvId, boolean onlyPublished) {
+    public List<Long> findAllDataverseDatasetChildren(Long dvId, boolean onlyPublished, boolean includeHarvested) {
         // get list of Dataverse children
         List<Long> dataverseChildren = findIdsByOwnerId(dvId);
         // get list of Dataset children
-        List<Long> datasetChildren = datasetService.findIdsByOwnerId(dvId, onlyPublished);
+        List<Long> datasetChildren = datasetService.findIdsByOwnerId(dvId, onlyPublished, includeHarvested);
         
         if (dataverseChildren == null) {
             return datasetChildren;
         } else {
             for (Long childDvId : dataverseChildren) {
-                datasetChildren.addAll(findAllDataverseDatasetChildren(childDvId, onlyPublished));
+                datasetChildren.addAll(findAllDataverseDatasetChildren(childDvId, onlyPublished, includeHarvested));
             }
             return datasetChildren;
         }
     }
 
     public List<Long> findAllDataverseDatasetChildren(Long dvId) {
-        return findAllDataverseDatasetChildren(dvId, false);
+        return findAllDataverseDatasetChildren(dvId, false, false);
     }
     
     public String addRoleAssignmentsToChildren(Dataverse owner, ArrayList<String> rolesToInherit,
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
index d7830991cff..75cdbf7bdd8 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
@@ -31,6 +31,7 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 import org.apache.commons.lang3.mutable.MutableBoolean;
+import org.apache.solr.client.solrj.SolrServerException;
 import org.xml.sax.SAXException;
 
 import io.gdcc.xoai.model.oaipmh.results.Record;
@@ -191,6 +192,12 @@ public void doHarvest(DataverseRequest dataverseRequest, Long harvestingClientId
 
                 hdLogger.log(Level.INFO, String.format("Datasets created/updated: %s, datasets deleted: %s, datasets failed: %s", harvestedDatasetIds.size(), deletedIdentifiers.size(), failedIdentifiers.size()));
 
+                // Reindex dataverse to update datasetCount
+                try {
+                    indexService.indexDataverse(harvestingClientConfig.getDataverse());
+                } catch (IOException | SolrServerException e) {
+                    hdLogger.log(Level.SEVERE, "Dataverse indexing failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + harvestingClientConfig.getDataverse().getId().toString());
+                }
             }
         } catch (StopHarvestException she) {
             hdLogger.log(Level.INFO, "HARVEST INTERRUPTED BY EXTERNAL REQUEST");
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
index 2f76fed1a11..7b8d6241dd1 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
@@ -7,6 +7,8 @@
 import edu.harvard.iq.dataverse.EjbDataverseEngine;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import edu.harvard.iq.dataverse.timer.DataverseTimerServiceBean;
+
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -22,6 +24,7 @@
 import jakarta.persistence.NoResultException;
 import jakarta.persistence.NonUniqueResultException;
 import jakarta.persistence.PersistenceContext;
+import org.apache.solr.client.solrj.SolrServerException;
 
 /**
  *
@@ -154,6 +157,14 @@ public void deleteClient(Long clientId) {
             }
 
             em.remove(merged);
+
+            // Reindex dataverse to update datasetCount
+            try {
+                indexService.indexDataverse(victim.getDataverse());
+            } catch (IOException | SolrServerException e) {
+                logger.severe("Dataverse indexing failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + victim.getDataverse().getId().toString());
+            }
+
         } catch (Exception e) {
             errorMessage = "Failed to delete cleint. Unknown exception: " + e.getMessage();
         }
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
index 4d50958da51..902c070c603 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
@@ -318,7 +318,7 @@ public Future<String> indexDataverse(Dataverse dataverse, boolean processPaths)
 
         if (dataverse.isReleased()) {
             // Get all datasets published in this dataverse, including harvested datasets
-            int numberOfPublishedDatasets = dataverseService.findAllDataverseDatasetChildren(dataverse.getId(), true).size();
+            int numberOfPublishedDatasets = dataverseService.findAllDataverseDatasetChildren(dataverse.getId(), true, true).size();
             // Get all published datasets linked to this dataverse
             int numberOfLinkedDatasets = dataverseService.findDatasetsThisIdHasLinkedTo(dataverse.getId(), true).size();
             solrInputDocument.addField(SearchFields.DATASET_COUNT, numberOfPublishedDatasets + numberOfLinkedDatasets);
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
index 44d033711ec..cd4a96420bd 100644
--- a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
+++ b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
@@ -1651,7 +1651,7 @@ public void testDataverseDatasetCounts() throws InterruptedException {
 
         // Wait for reindex of dataverse after publishing
         String searchEmptyDataverseQuery = "identifier:" + dataverseAlias + " AND publicationStatus:Published AND datasetCount:0";
-        assertTrue(UtilIT.sleepForSearch(searchEmptyDataverseQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+        assertTrue(UtilIT.sleepForSearch(searchEmptyDataverseQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
 
         Response searchEmptyDataverse = UtilIT.search(searchEmptyDataverseQuery, apiToken, "&type=dataverse");
         searchEmptyDataverse.prettyPrint();
@@ -1674,7 +1674,7 @@ public void testDataverseDatasetCounts() throws InterruptedException {
 
         // Wait for reindex of dataverse after publishing
         String searchDataverseWithDatasetQuery = "identifier:" + dataverseAlias + " AND datasetCount:1";
-        assertTrue(UtilIT.sleepForSearch(searchDataverseWithDatasetQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
 
         Response searchDataverseWithDataset = UtilIT.search(searchDataverseWithDatasetQuery, apiToken, "&type=dataverse");
         searchDataverseWithDataset.prettyPrint();
@@ -1694,7 +1694,7 @@ public void testDataverseDatasetCounts() throws InterruptedException {
 
         // Wait for reindex of dataverse after publishing
         String searchEmptyDataverse2Query = "identifier:" + dataverseAlias2 + " AND publicationStatus:Published AND datasetCount:0";
-        assertTrue(UtilIT.sleepForSearch(searchEmptyDataverse2Query, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+        assertTrue(UtilIT.sleepForSearch(searchEmptyDataverse2Query, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
 
         Response searchEmptyDataverse2 = UtilIT.search(searchEmptyDataverse2Query, apiToken, "&type=dataverse");
         searchEmptyDataverse2.prettyPrint();
@@ -1712,7 +1712,7 @@ public void testDataverseDatasetCounts() throws InterruptedException {
 
         // Wait for reindex of dataverse after linking
         String searchDataverseWithLinkedDatasetQuery = "identifier:" + dataverseAlias2 + " AND datasetCount:1";
-        assertTrue(UtilIT.sleepForSearch(searchDataverseWithLinkedDatasetQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithLinkedDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
 
         Response searchDataverseWithLinkedDataset = UtilIT.search(searchDataverseWithLinkedDatasetQuery, apiToken, "&type=dataverse");
         searchDataverseWithLinkedDataset.prettyPrint();
@@ -1723,103 +1723,119 @@ public void testDataverseDatasetCounts() throws InterruptedException {
                 .body("data.items[0].datasetCount", CoreMatchers.equalTo(1));
 
         // Check that harvested datasets are counted
-        // TODO Harvesting fails with "lastResult": "Completed with failures",
-//        Response createDataverseResponse3 = UtilIT.createRandomDataverse(apiToken);
-//        createDataverseResponse3.prettyPrint();
-//        String dataverseAlias3 = UtilIT.getAliasFromResponse(createDataverseResponse3);
-//
-//        Response publishDataverse3 = UtilIT.publishDataverseViaNativeApi(dataverseAlias3, apiToken);
-//        publishDataverse3.then().assertThat()
-//                .statusCode(OK.getStatusCode());
-//
-//        String nickName = "h" + UtilIT.getRandomString(6);
-//        String sourceName = "";
-//
-//        String clientApiPath = String.format("/api/harvest/clients/%s", nickName);
-//        String clientJson = String.format("{\"dataverseAlias\":\"%s\","
-//                        + "\"type\":\"oai\","
-//                        + "\"sourceName\":\"%s\","
-//                        + "\"harvestUrl\":\"%s\","
-//                        + "\"archiveUrl\":\"%s\","
-//                        + "\"set\":\"%s\","
-//                        + "\"allowHarvestingMissingCVV\":%s,"
-//                        + "\"metadataFormat\":\"%s\"}",
-//                dataverseAlias3, sourceName, "https://demo.dataverse.org/oai", "https://demo.dataverse.org",
-//                "controlTestSet2", false, "oai_dc");
-//
-//        Response createResponse = given()
-//                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
-//                .body(clientJson)
-//                .post(clientApiPath);
-//        createResponse.prettyPrint();
-//        assertEquals(CREATED.getStatusCode(), createResponse.getStatusCode());
-//
-//        String runHarvestApiPath = String.format("/api/harvest/clients/%s/run", nickName);
-//
-//        Response runResponse = given()
-//                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
-//                .post(runHarvestApiPath);
-//        runResponse.prettyPrint();
-//        assertEquals(ACCEPTED.getStatusCode(), runResponse.getStatusCode());
-//
-//        int i = 0;
-//        int maxWait=20; // a very conservative interval; this harvest has no business taking this long
-//        int numberOfDatasetsHarvested = 0;
-//        do {
-//            // Give it an initial 2 sec. delay, to make sure the client state
-//            // has been updated in the database, which can take some appreciable
-//            // amount of time on a heavily-loaded server running a full suite of
-//            // tests:
-//            Thread.sleep(2000L);
-//            // keep checking the status of the client with the GET api:
-//            Response getClientResponse = given()
-//                    .get(clientApiPath);
-//
-//            assertEquals(OK.getStatusCode(), getClientResponse.getStatusCode());
-//            JsonPath responseJsonPath = getClientResponse.body().jsonPath();
-//            assertNotNull(responseJsonPath, "Invalid JSON in GET client response");
-//            assertEquals(ApiConstants.STATUS_OK, responseJsonPath.getString("status"));
-//
-//            String clientStatus = responseJsonPath.getString("data.status");
-//            assertNotNull(clientStatus);
-//
-//            if ("inProgress".equals(clientStatus) || "IN PROGRESS".equals(responseJsonPath.getString("data.lastResult"))) {
-//                // we'll sleep for 2 more seconds
-//                i++;
-//            } else {
-//                logger.info("getClientResponse.prettyPrint: "
-//                        + getClientResponse.prettyPrint());
-//                // Check the values in the response:
-//                // a) Confirm that the harvest has completed:
-//                assertEquals("inActive", clientStatus, "Unexpected client status: "+clientStatus);
-//
-//                // b) Confirm that it has actually succeeded:
-//                assertTrue(responseJsonPath.getString("data.lastResult").contains("Completed"), "Last harvest not reported a success (took "+i+" seconds)");
-//                String harvestTimeStamp = responseJsonPath.getString("data.lastHarvest");
-//                assertNotNull(harvestTimeStamp);
-//
-//                // c) Confirm that at least one dataset has been harvested:
-//                numberOfDatasetsHarvested = responseJsonPath.getInt("data.lastDatasetsHarvested");
-//                assertTrue(numberOfDatasetsHarvested > 0);
-//
-//                // ok, it looks like the harvest has completed successfully.
-//                break;
-//            }
-//        } while (i<maxWait);
-//
-//        System.out.println("Waited " + i + " seconds for the harvest to complete.");
-//
-//        // Wait for reindex of dataverse after harvesting
-//        String searchDataverseWithHarvestedDatasetQuery = "identifier:" + dataverseAlias3 + " AND datasetCount:" + numberOfDatasetsHarvested;
-//        assertTrue(UtilIT.sleepForSearch(searchDataverseWithHarvestedDatasetQuery, null, null, 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
-//
-//        Response searchDataverseWithHarvestedDataset = UtilIT.search(searchDataverseWithHarvestedDatasetQuery, apiToken, "&type=dataverse");
-//        searchDataverseWithHarvestedDataset.prettyPrint();
-//        searchDataverseWithHarvestedDataset.then().assertThat()
-//                .statusCode(OK.getStatusCode())
-//                .body("data.total_count", CoreMatchers.equalTo(1))
-//                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias3))
-//                .body("data.items[0].datasetCount", CoreMatchers.equalTo(numberOfDatasetsHarvested));
+        Response createDataverseResponse3 = UtilIT.createRandomDataverse(apiToken);
+        createDataverseResponse3.prettyPrint();
+        String dataverseAlias3 = UtilIT.getAliasFromResponse(createDataverseResponse3);
+
+        Response publishDataverse3 = UtilIT.publishDataverseViaNativeApi(dataverseAlias3, apiToken);
+        publishDataverse3.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        String nickName = "h" + UtilIT.getRandomString(6);
+        String sourceName = "";
+
+        String clientApiPath = String.format("/api/harvest/clients/%s", nickName);
+        String clientJson = String.format("{\"dataverseAlias\":\"%s\","
+                        + "\"type\":\"oai\","
+                        + "\"sourceName\":\"%s\","
+                        + "\"harvestUrl\":\"%s\","
+                        + "\"archiveUrl\":\"%s\","
+                        + "\"set\":\"%s\","
+                        + "\"allowHarvestingMissingCVV\":%s,"
+                        + "\"metadataFormat\":\"%s\"}",
+                dataverseAlias3, sourceName, "https://demo.dataverse.org/oai", "https://demo.dataverse.org",
+                "controlTestSet2", true, "oai_dc");
+
+        Response createResponse = given()
+                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
+                .body(clientJson)
+                .post(clientApiPath);
+        createResponse.prettyPrint();
+        assertEquals(CREATED.getStatusCode(), createResponse.getStatusCode());
+
+        String runHarvestApiPath = String.format("/api/harvest/clients/%s/run", nickName);
+
+        Response runResponse = given()
+                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
+                .post(runHarvestApiPath);
+        runResponse.prettyPrint();
+        assertEquals(ACCEPTED.getStatusCode(), runResponse.getStatusCode());
+
+        int i = 0;
+        int maxWait=20; // a very conservative interval; this harvest has no business taking this long
+        int numberOfDatasetsHarvested = 0;
+        do {
+            // Give it an initial 2 sec. delay, to make sure the client state
+            // has been updated in the database, which can take some appreciable
+            // amount of time on a heavily-loaded server running a full suite of
+            // tests:
+            Thread.sleep(2000L);
+            // keep checking the status of the client with the GET api:
+            Response getClientResponse = given()
+                    .get(clientApiPath);
+
+            assertEquals(OK.getStatusCode(), getClientResponse.getStatusCode());
+            JsonPath responseJsonPath = getClientResponse.body().jsonPath();
+            assertNotNull(responseJsonPath, "Invalid JSON in GET client response");
+            assertEquals(ApiConstants.STATUS_OK, responseJsonPath.getString("status"));
+
+            String clientStatus = responseJsonPath.getString("data.status");
+            assertNotNull(clientStatus);
+
+            if ("inProgress".equals(clientStatus) || "IN PROGRESS".equals(responseJsonPath.getString("data.lastResult"))) {
+                // we'll sleep for 2 more seconds
+                i++;
+            } else {
+                logger.info("getClientResponse.prettyPrint: "
+                        + getClientResponse.prettyPrint());
+                // Check the values in the response:
+                // a) Confirm that the harvest has completed:
+                assertEquals("inActive", clientStatus, "Unexpected client status: "+clientStatus);
+
+                // b) Confirm that it has actually succeeded:
+                assertTrue(responseJsonPath.getString("data.lastResult").contains("Completed"), "Last harvest not reported a success (took "+i+" seconds)");
+                String harvestTimeStamp = responseJsonPath.getString("data.lastHarvest");
+                assertNotNull(harvestTimeStamp);
+
+                // c) Confirm that at least one dataset has been harvested:
+                numberOfDatasetsHarvested = responseJsonPath.getInt("data.lastDatasetsHarvested");
+                assertTrue(numberOfDatasetsHarvested > 0);
+
+                // ok, it looks like the harvest has completed successfully.
+                break;
+            }
+        } while (i<maxWait);
+
+        System.out.println("Waited " + i + " seconds for the harvest to complete.");
+
+        // Wait for reindex of dataverse after harvesting
+        String searchDataverseWithHarvestedDatasetQuery = "identifier:" + dataverseAlias3 + " AND datasetCount:" + numberOfDatasetsHarvested;
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithHarvestedDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithHarvestedDataset = UtilIT.search(searchDataverseWithHarvestedDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithHarvestedDataset.prettyPrint();
+        searchDataverseWithHarvestedDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias3))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(numberOfDatasetsHarvested));
+
+        // Clean up harvesting client and harvested datasets
+        Response deleteResponse = given()
+                .header(UtilIT.API_TOKEN_HTTP_HEADER, apiToken)
+                .delete(clientApiPath);
+        deleteResponse.prettyPrint();
+
+        String searchDataverseWithNoMoreHarvestedDatasetsQuery = "identifier:" + dataverseAlias3 + " AND datasetCount:0";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithNoMoreHarvestedDatasetsQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithNoMoreHarvestedDatasets = UtilIT.search(searchDataverseWithNoMoreHarvestedDatasetsQuery, apiToken, "&type=dataverse");
+        searchDataverseWithNoMoreHarvestedDatasets.prettyPrint();
+        searchDataverseWithNoMoreHarvestedDatasets.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias3))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
     }
 
     @AfterEach

From 909a738794714782086d437235c6940584c72fdf Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Thu, 5 Jun 2025 13:47:47 +0200
Subject: [PATCH 05/11] feat: don't include unlinked or destroyed datasets in
 datasetCount

---
 .../command/impl/DestroyDatasetCommand.java   | 22 +++++---
 .../harvard/iq/dataverse/api/SearchIT.java    | 55 +++++++++++++++++++
 2 files changed, 68 insertions(+), 9 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
index be3e28029e4..7228312bc48 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
@@ -49,12 +49,13 @@ public class DestroyDatasetCommand extends AbstractVoidCommand {
     
     private List<String> datasetAndFileSolrIdsToDelete; 
     
-    private Dataverse toReIndex;
+    private List<Dataverse> toReIndex;
 
     public DestroyDatasetCommand(Dataset doomed, DataverseRequest aRequest) {
         super(aRequest, doomed);
         this.doomed = doomed;
         datasetAndFileSolrIdsToDelete = new ArrayList<>();
+        toReIndex = new ArrayList<>();
     }
 
     @Override
@@ -116,7 +117,8 @@ protected void executeImpl(CommandContext ctxt) throws CommandException {
             }
         }
         
-        toReIndex = managedDoomed.getOwner();
+        toReIndex.add(managedDoomed.getOwner());
+        managedDoomed.getDatasetLinkingDataverses().forEach(dld -> toReIndex.add(dld.getLinkingDataverse()));
 
         // add potential Solr IDs of datasets to list for deletion
         String solrIdOfPublishedDatasetVersion = IndexServiceBean.solrDocIdentifierDataset + managedDoomed.getId();
@@ -145,13 +147,15 @@ public boolean onSuccess(CommandContext ctxt, Object r) {
         logger.log(Level.FINE, "Result of attempt to delete dataset and file IDs from the search index: {0}", resultOfSolrDeletionAttempt.getMessage());
 
         // reindex
-        try {
-            ctxt.index().indexDataverse(toReIndex);                   
-        } catch (IOException | SolrServerException e) {    
-            String failureLogText = "Post-destroy dataset indexing of the owning dataverse failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + toReIndex.getId().toString();
-            failureLogText += "\r\n" + e.getLocalizedMessage();
-            LoggingUtil.writeOnSuccessFailureLog(this, failureLogText,  toReIndex);
-            retVal = false;
+        for (Dataverse dv : toReIndex) {
+            try {
+                    ctxt.index().indexDataverse(dv);
+            } catch (IOException | SolrServerException e) {
+                String failureLogText = "Post-destroy dataset indexing of an owning or linking dataverse failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + dv.getId().toString();
+                failureLogText += "\r\n" + e.getLocalizedMessage();
+                LoggingUtil.writeOnSuccessFailureLog(this, failureLogText,  dv);
+                retVal = false;
+            }
         }
         
         return retVal;
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
index cd4a96420bd..8ba1c75eba8 100644
--- a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
+++ b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
@@ -1722,6 +1722,61 @@ public void testDataverseDatasetCounts() throws InterruptedException {
                 .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias2))
                 .body("data.items[0].datasetCount", CoreMatchers.equalTo(1));
 
+        // Check that unlinked datasets are no longer counted
+        Response unlinkDataset = UtilIT.deleteDatasetLink(Long.valueOf(datasetId), dataverseAlias2, apiToken);
+        unlinkDataset.prettyPrint();
+        unlinkDataset.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Wait for reindex of dataverse after unlinking
+        String searchDataverseWithUnlinkedDatasetQuery = "identifier:" + dataverseAlias2 + " AND datasetCount:0";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithUnlinkedDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithUnlinkedDataset = UtilIT.search(searchDataverseWithUnlinkedDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithUnlinkedDataset.prettyPrint();
+        searchDataverseWithUnlinkedDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias2))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
+
+        // Re-link dataset
+        Response linkDatasetAgain = UtilIT.linkDataset(datasetPid, dataverseAlias2, apiToken);
+        linkDatasetAgain.prettyPrint();
+        linkDatasetAgain.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Wait for reindex of dataverse after linking
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithLinkedDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        // Check that destroyed datasets are no longer counted
+        Response destroyDataset = UtilIT.destroyDataset(datasetPid, apiToken);
+        destroyDataset.prettyPrint();
+        destroyDataset.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Wait for reindex of dataverses after destroying dataset
+        String searchDataverseWithDestroyedDatasetQuery = "identifier:" + dataverseAlias + " AND datasetCount:0";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithDestroyedDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+        String searchDataverseWithDestroyedLinkedDatasetQuery = "identifier:" + dataverseAlias2 + " AND datasetCount:0";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithDestroyedLinkedDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithDestroyedDataset = UtilIT.search(searchDataverseWithDestroyedDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithDestroyedDataset.prettyPrint();
+        searchDataverseWithDestroyedDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
+
+        Response searchDataverseWithDestroyedLinkedDataset = UtilIT.search(searchDataverseWithDestroyedLinkedDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithDestroyedLinkedDataset.prettyPrint();
+        searchDataverseWithDestroyedLinkedDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias2))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
+
         // Check that harvested datasets are counted
         Response createDataverseResponse3 = UtilIT.createRandomDataverse(apiToken);
         createDataverseResponse3.prettyPrint();

From 6d302bafb42bec487a89ae593ec64a29bc142c61 Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Thu, 5 Jun 2025 14:10:50 +0200
Subject: [PATCH 06/11] docs: update release note for datasetCount

---
 doc/release-notes/10190-dataset-count.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/release-notes/10190-dataset-count.md b/doc/release-notes/10190-dataset-count.md
index 5da89edcdb6..a3d3a052f87 100644
--- a/doc/release-notes/10190-dataset-count.md
+++ b/doc/release-notes/10190-dataset-count.md
@@ -1,2 +1,2 @@
-The search index now includes datasetCount for each collection, counting both published and linked datasets.
+The search index now includes datasetCount for each collection, counting published, linked, and harvested datasets.
 Collections can be filtered using datasetCount (e.g., `datasetCount:[1000 TO *]`), and the value is returned in Dataverse search results via the Search API.
\ No newline at end of file

From 7eee55eefe04b5191c7cfa0cf652791608ef56c8 Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Thu, 5 Jun 2025 16:02:39 +0200
Subject: [PATCH 07/11] fix: improve code + add comments in findIdsByOwnerId

---
 .../harvard/iq/dataverse/DatasetServiceBean.java | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
index cb726b2ccd8..f36a8ea772f 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -178,10 +178,18 @@ public List<Long> findIdsByOwnerId(Long ownerId, boolean onlyPublished, boolean
             List<Dataset> results = em.createNamedQuery("Dataset.findByOwnerId")
                     .setParameter("ownerId", ownerId).getResultList();
             for (Dataset ds : results) {
-                if (onlyPublished && ds.isReleased() && !ds.isDeaccessioned()) {
-                    retList.add(ds.getId());
-                } else if (includeHarvested && ds.isHarvested()) {
-                    retList.add(ds.getId());
+                // For harvested datasets, only add them if includeHarvested is true
+                if (ds.isHarvested()) {
+                    if (includeHarvested) {
+                        retList.add(ds.getId());
+                    }
+                // For non-harvested datasets, either
+                // - add them all (if onlyPublished is false) OR
+                // - only add them if they are released and not deaccessioned (if onlyPublished is true)
+                } else {
+                    if (!onlyPublished || (ds.isReleased() && !ds.isDeaccessioned())) {
+                        retList.add(ds.getId());
+                    }
                 }
             }
             return retList;

From d8a28f3e4b96d8ad3d62d52bd6c781a0998600aa Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Thu, 12 Jun 2025 14:50:02 +0200
Subject: [PATCH 08/11] feat: reindex linking dataverses when dataset is
 published

---
 .../impl/FinalizeDatasetPublicationCommand.java      | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
index fa8cfeb810a..a2e7e85e259 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
@@ -28,8 +28,7 @@
 import edu.harvard.iq.dataverse.workflow.WorkflowContext.TriggerType;
 import java.io.IOException;
 import java.sql.Timestamp;
-import java.util.Date;
-import java.util.List;
+import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -37,7 +36,7 @@
 import edu.harvard.iq.dataverse.dataaccess.StorageIO;
 import edu.harvard.iq.dataverse.engine.command.Command;
 import edu.harvard.iq.dataverse.util.FileUtil;
-import java.util.ArrayList;
+
 import java.util.concurrent.Future;
 import org.apache.solr.client.solrj.SolrServerException;
 
@@ -60,7 +59,7 @@ public class FinalizeDatasetPublicationCommand extends AbstractPublishDatasetCom
      */
     final boolean datasetExternallyReleased;
     
-    List<Dataverse> dataversesToIndex = new ArrayList<>();
+    Set<Dataverse> dataversesToIndex = new HashSet<>();
     
     public static final String FILE_VALIDATION_ERROR = "FILE VALIDATION ERROR";
     
@@ -198,6 +197,11 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
 
         }
 
+        // The owning dataverse plus all dataverses linking to this dataset must be re-indexed to update their
+        // datasetCount
+        dataversesToIndex.add(getDataset().getOwner());
+        getDataset().getDatasetLinkingDataverses().forEach(dld -> dataversesToIndex.add(dld.getLinkingDataverse()));
+
         List<Command> previouslyCalled = ctxt.getCommandsCalled();
         
         PrivateUrl privateUrl = ctxt.engine().submit(new GetPrivateUrlCommand(getRequest(), theDataset));

From fbc23cd8475288b194ac8574699af1fcd010996a Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Tue, 24 Jun 2025 10:50:30 +0200
Subject: [PATCH 09/11] feat: improve performance of calculating datasetCount
 using named query

---
 .../java/edu/harvard/iq/dataverse/Dataverse.java   |  8 +++++++-
 .../harvard/iq/dataverse/DataverseServiceBean.java | 14 ++++++++++++++
 .../iq/dataverse/search/IndexServiceBean.java      |  6 +-----
 3 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
index 8ab6f537aca..d4165601cda 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
@@ -56,7 +56,13 @@
     @NamedQuery(name = "Dataverse.filterByAlias", query="SELECT dv FROM Dataverse dv WHERE LOWER(dv.alias) LIKE :alias order by dv.alias"),
     @NamedQuery(name = "Dataverse.filterByAliasNameAffiliation", query="SELECT dv FROM Dataverse dv WHERE (LOWER(dv.alias) LIKE :alias) OR (LOWER(dv.name) LIKE :name) OR (LOWER(dv.affiliation) LIKE :affiliation) order by dv.alias"),
     @NamedQuery(name = "Dataverse.filterByName", query="SELECT dv FROM Dataverse dv WHERE LOWER(dv.name) LIKE :name  order by dv.alias"),
-    @NamedQuery(name = "Dataverse.countAll", query = "SELECT COUNT(dv) FROM Dataverse dv")
+    @NamedQuery(name = "Dataverse.countAll", query = "SELECT COUNT(dv) FROM Dataverse dv"),
+    @NamedQuery(name = "Dataverse.getDatasetCount",
+                query = "SELECT " +
+                        "(SELECT COUNT(DISTINCT d) FROM Dataset d JOIN d.versions v WHERE d.owner.id = :id AND v.versionState = :datasetState) + " +
+                        "(SELECT COUNT(DISTINCT l.dataset) FROM DatasetLinkingDataverse l JOIN l.dataset.versions v WHERE l.linkingDataverse.id = :id AND v.versionState = :datasetState) " +
+                        // The WHERE statement is a hacky way of ensuring the count is returned in a single result row
+                        "FROM Dataverse d WHERE d.id = (SELECT MIN(d2.id) FROM Dataverse d2)")
 })
 @Entity
 @Table(indexes = {@Index(columnList="defaultcontributorrole_id")
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
index 91d4e861e15..db601f4bbef 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
@@ -14,6 +14,7 @@
 import edu.harvard.iq.dataverse.authorization.users.User;
 import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
 import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
+import edu.harvard.iq.dataverse.DatasetVersion.VersionState;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import edu.harvard.iq.dataverse.search.SolrIndexServiceBean;
@@ -1279,4 +1280,17 @@ public void disableStorageQuota(StorageQuota storageQuota) {
     public long getDataverseCount() {
         return em.createNamedQuery("Dataverse.countAll", Long.class).getSingleResult();
     }
+
+    /**
+     * Returns the total number of published datasets within a Dataverse collection, including harvested and linked
+     * datasets.
+     * @param dvId ID of a Dataverse collection
+     * @return the total number of published datasets within that Dataverse collection
+     */
+    public long getDatasetCount(Long dvId) {
+        return em.createNamedQuery("Dataverse.getDatasetCount", Long.class)
+                 .setParameter("id", dvId)
+                 .setParameter("datasetState", VersionState.RELEASED)
+                 .getSingleResult();
+    }
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
index 902c070c603..542fb08d7f7 100644
--- a/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/search/IndexServiceBean.java
@@ -317,11 +317,7 @@ public Future<String> indexDataverse(Dataverse dataverse, boolean processPaths)
         solrInputDocument.addField(SearchFields.SUBTREE, dataversePaths);
 
         if (dataverse.isReleased()) {
-            // Get all datasets published in this dataverse, including harvested datasets
-            int numberOfPublishedDatasets = dataverseService.findAllDataverseDatasetChildren(dataverse.getId(), true, true).size();
-            // Get all published datasets linked to this dataverse
-            int numberOfLinkedDatasets = dataverseService.findDatasetsThisIdHasLinkedTo(dataverse.getId(), true).size();
-            solrInputDocument.addField(SearchFields.DATASET_COUNT, numberOfPublishedDatasets + numberOfLinkedDatasets);
+            solrInputDocument.addField(SearchFields.DATASET_COUNT, dataverseService.getDatasetCount(dataverse.getId()));
         }
 
         docs.add(solrInputDocument);

From b29972be77305c33659b334ca1ee924dfc436e88 Mon Sep 17 00:00:00 2001
From: Vera Clemens <clemens@zbmed.de>
Date: Thu, 3 Jul 2025 13:00:16 +0200
Subject: [PATCH 10/11] feat: include datasets in sub-dataverses in
 datasetCount

---
 .../edu/harvard/iq/dataverse/Dataverse.java   |  4 +-
 .../iq/dataverse/DataverseServiceBean.java    | 32 +++++++++++-----
 .../DeleteDatasetLinkingDataverseCommand.java | 20 +++++++---
 .../command/impl/DestroyDatasetCommand.java   |  6 ++-
 .../FinalizeDatasetPublicationCommand.java    |  6 ++-
 .../command/impl/LinkDatasetCommand.java      | 23 +++++++----
 .../harvest/client/HarvesterServiceBean.java  | 13 +++++--
 .../client/HarvestingClientServiceBean.java   | 19 +++++-----
 .../harvard/iq/dataverse/api/SearchIT.java    | 38 +++++++++++++++++++
 9 files changed, 121 insertions(+), 40 deletions(-)

diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
index d4165601cda..a5de4e4e6b5 100644
--- a/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
+++ b/src/main/java/edu/harvard/iq/dataverse/Dataverse.java
@@ -59,8 +59,8 @@
     @NamedQuery(name = "Dataverse.countAll", query = "SELECT COUNT(dv) FROM Dataverse dv"),
     @NamedQuery(name = "Dataverse.getDatasetCount",
                 query = "SELECT " +
-                        "(SELECT COUNT(DISTINCT d) FROM Dataset d JOIN d.versions v WHERE d.owner.id = :id AND v.versionState = :datasetState) + " +
-                        "(SELECT COUNT(DISTINCT l.dataset) FROM DatasetLinkingDataverse l JOIN l.dataset.versions v WHERE l.linkingDataverse.id = :id AND v.versionState = :datasetState) " +
+                        "(SELECT COUNT(DISTINCT d) FROM Dataset d JOIN d.versions v WHERE d.owner.id IN :ids AND v.versionState = :datasetState) + " +
+                        "(SELECT COUNT(DISTINCT l.dataset) FROM DatasetLinkingDataverse l JOIN l.dataset.versions v WHERE l.linkingDataverse.id IN :ids AND v.versionState = :datasetState) " +
                         // The WHERE statement is a hacky way of ensuring the count is returned in a single result row
                         "FROM Dataverse d WHERE d.id = (SELECT MIN(d2.id) FROM Dataverse d2)")
 })
diff --git a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
index db601f4bbef..0247ad5aa15 100644
--- a/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java
@@ -27,13 +27,8 @@
 import java.io.File;
 import java.io.IOException;
 import java.sql.Timestamp;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.logging.Logger;
-import java.util.Properties;
 
 import edu.harvard.iq.dataverse.validation.JSONDataValidation;
 import jakarta.ejb.EJB;
@@ -1282,14 +1277,33 @@ public long getDataverseCount() {
     }
 
     /**
-     * Returns the total number of published datasets within a Dataverse collection, including harvested and linked
-     * datasets.
+     * Returns the total number of published datasets within a Dataverse collection. The number includes harvested and
+     * linked datasets. Datasets in subcollections are also counted.
      * @param dvId ID of a Dataverse collection
      * @return the total number of published datasets within that Dataverse collection
      */
     public long getDatasetCount(Long dvId) {
+        Set<Long> dvIds = new HashSet<>();
+        Deque<Long> stack = new ArrayDeque<>();
+        dvIds.add(dvId);
+        stack.push(dvId);
+
+        // Collect IDs of all subdataverses
+        while (!stack.isEmpty()) {
+            Long currentId = stack.pop();
+            List<Long> children = em.createQuery("SELECT d.id FROM Dataverse d WHERE d.owner.id = :parentId", Long.class)
+                                    .setParameter("parentId", currentId)
+                                    .getResultList();
+
+            for (Long childId : children) {
+                if (dvIds.add(childId)) {
+                    stack.push(childId);
+                }
+            }
+        }
+
         return em.createNamedQuery("Dataverse.getDatasetCount", Long.class)
-                 .setParameter("id", dvId)
+                 .setParameter("ids", dvIds)
                  .setParameter("datasetState", VersionState.RELEASED)
                  .getSingleResult();
     }
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeleteDatasetLinkingDataverseCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeleteDatasetLinkingDataverseCommand.java
index 7f5672c0cd7..d44638be42c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeleteDatasetLinkingDataverseCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeleteDatasetLinkingDataverseCommand.java
@@ -7,6 +7,7 @@
 
 import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.DatasetLinkingDataverse;
+import edu.harvard.iq.dataverse.Dataverse;
 import edu.harvard.iq.dataverse.authorization.Permission;
 import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
 import edu.harvard.iq.dataverse.engine.command.AbstractCommand;
@@ -15,6 +16,8 @@
 import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.solr.client.solrj.SolrServerException;
 
@@ -42,12 +45,17 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
         DatasetLinkingDataverse doomedAndMerged = ctxt.em().merge(doomed);
         ctxt.em().remove(doomedAndMerged);
 
-        try {
-            ctxt.index().indexDataverse(doomed.getLinkingDataverse());
-        } catch (IOException | SolrServerException e) {    
-            String failureLogText = "Post delete linking dataverse indexing failed for Dataverse. ";
-            failureLogText += "\r\n" + e.getLocalizedMessage();
-            LoggingUtil.writeOnSuccessFailureLog(this, failureLogText,  doomed.getLinkingDataverse());
+        List<Dataverse> toReindex = new ArrayList<>();
+        toReindex.add(doomed.getLinkingDataverse());
+        toReindex.addAll(doomed.getLinkingDataverse().getOwners());
+        for (Dataverse dv : toReindex) {
+            try {
+                ctxt.index().indexDataverse(dv);
+            } catch (IOException | SolrServerException e) {
+                String failureLogText = "Post delete linking dataverse indexing failed for Dataverse. ";
+                failureLogText += "\r\n" + e.getLocalizedMessage();
+                LoggingUtil.writeOnSuccessFailureLog(this, failureLogText, dv);
+            }
         }
 
         return merged;
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
index 7228312bc48..14dafd8397c 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
@@ -118,7 +118,11 @@ protected void executeImpl(CommandContext ctxt) throws CommandException {
         }
         
         toReIndex.add(managedDoomed.getOwner());
-        managedDoomed.getDatasetLinkingDataverses().forEach(dld -> toReIndex.add(dld.getLinkingDataverse()));
+        toReIndex.addAll(managedDoomed.getOwner().getOwners());
+        managedDoomed.getDatasetLinkingDataverses().forEach(dld -> {
+            toReIndex.add(dld.getLinkingDataverse());
+            toReIndex.addAll(dld.getLinkingDataverse().getOwners());
+        });
 
         // add potential Solr IDs of datasets to list for deletion
         String solrIdOfPublishedDatasetVersion = IndexServiceBean.solrDocIdentifierDataset + managedDoomed.getId();
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
index a2e7e85e259..e93e4755aab 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
@@ -200,7 +200,11 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
         // The owning dataverse plus all dataverses linking to this dataset must be re-indexed to update their
         // datasetCount
         dataversesToIndex.add(getDataset().getOwner());
-        getDataset().getDatasetLinkingDataverses().forEach(dld -> dataversesToIndex.add(dld.getLinkingDataverse()));
+        dataversesToIndex.addAll(getDataset().getOwner().getOwners());
+        getDataset().getDatasetLinkingDataverses().forEach(dld -> {
+            dataversesToIndex.add(dld.getLinkingDataverse());
+            dataversesToIndex.addAll(dld.getLinkingDataverse().getOwners());
+        });
 
         List<Command> previouslyCalled = ctxt.getCommandsCalled();
         
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java
index 54630f3e64e..81de3efbc95 100644
--- a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java
+++ b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/LinkDatasetCommand.java
@@ -19,7 +19,10 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.IOException;
 import java.sql.Timestamp;
+import java.util.ArrayList;
 import java.util.Date;
+import java.util.List;
+
 import org.apache.solr.client.solrj.SolrServerException;
 
 /**
@@ -71,14 +74,18 @@ public boolean onSuccess(CommandContext ctxt, Object r) {
 
         ctxt.index().asyncIndexDataset(dld.getDataset(), true);
 
-        Dataverse linkingDataverse = dld.getLinkingDataverse();
-        try {
-            ctxt.index().indexDataverse(linkingDataverse);
-        } catch (IOException | SolrServerException e) {
-            String failureLogText = "Indexing of linking dataverse failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + linkingDataverse.getId().toString();
-            failureLogText += "\r\n" + e.getLocalizedMessage();
-            LoggingUtil.writeOnSuccessFailureLog(null, failureLogText, linkingDataverse);
-            return false;
+        List<Dataverse> toReindex = new ArrayList<>();
+        toReindex.add(dld.getLinkingDataverse());
+        toReindex.addAll(dld.getLinkingDataverse().getOwners());
+        for (Dataverse dv : toReindex) {
+            try {
+                ctxt.index().indexDataverse(dv);
+            } catch (IOException | SolrServerException e) {
+                String failureLogText = "Indexing of linking dataverse failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + dv.getId().toString();
+                failureLogText += "\r\n" + e.getLocalizedMessage();
+                LoggingUtil.writeOnSuccessFailureLog(null, failureLogText, dv);
+                return false;
+            }
         }
 
         return retVal;
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
index 75cdbf7bdd8..a1976b612fa 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvesterServiceBean.java
@@ -193,10 +193,15 @@ public void doHarvest(DataverseRequest dataverseRequest, Long harvestingClientId
                 hdLogger.log(Level.INFO, String.format("Datasets created/updated: %s, datasets deleted: %s, datasets failed: %s", harvestedDatasetIds.size(), deletedIdentifiers.size(), failedIdentifiers.size()));
 
                 // Reindex dataverse to update datasetCount
-                try {
-                    indexService.indexDataverse(harvestingClientConfig.getDataverse());
-                } catch (IOException | SolrServerException e) {
-                    hdLogger.log(Level.SEVERE, "Dataverse indexing failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + harvestingClientConfig.getDataverse().getId().toString());
+                List<Dataverse> toReindex = new ArrayList<>();
+                toReindex.add(harvestingClientConfig.getDataverse());
+                toReindex.addAll(harvestingClientConfig.getDataverse().getOwners());
+                for (Dataverse dv : toReindex) {
+                    try {
+                        indexService.indexDataverse(dv);
+                    } catch (IOException | SolrServerException e) {
+                        hdLogger.log(Level.SEVERE, "Dataverse indexing failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + dv.getId().toString());
+                    }
                 }
             }
         } catch (StopHarvestException she) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
index 7b8d6241dd1..4b491a5e722 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/HarvestingClientServiceBean.java
@@ -1,10 +1,6 @@
 package edu.harvard.iq.dataverse.harvest.client;
 
-import edu.harvard.iq.dataverse.DataFile;
-import edu.harvard.iq.dataverse.DataFileServiceBean;
-import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
-import edu.harvard.iq.dataverse.DataverseServiceBean;
-import edu.harvard.iq.dataverse.EjbDataverseEngine;
+import edu.harvard.iq.dataverse.*;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import edu.harvard.iq.dataverse.timer.DataverseTimerServiceBean;
 
@@ -159,10 +155,15 @@ public void deleteClient(Long clientId) {
             em.remove(merged);
 
             // Reindex dataverse to update datasetCount
-            try {
-                indexService.indexDataverse(victim.getDataverse());
-            } catch (IOException | SolrServerException e) {
-                logger.severe("Dataverse indexing failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + victim.getDataverse().getId().toString());
+            List<Dataverse> toReindex = new ArrayList<>();
+            toReindex.add(victim.getDataverse());
+            toReindex.addAll(victim.getDataverse().getOwners());
+            for (Dataverse dv : toReindex) {
+                try {
+                    indexService.indexDataverse(dv);
+                } catch (IOException | SolrServerException e) {
+                    logger.severe("Dataverse indexing failed. You can kickoff a re-index of this dataverse with: \r\n curl http://localhost:8080/api/admin/index/dataverses/" + dv.getId().toString());
+                }
             }
 
         } catch (Exception e) {
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
index 8ba1c75eba8..e1d9533fa7e 100644
--- a/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
+++ b/src/test/java/edu/harvard/iq/dataverse/api/SearchIT.java
@@ -1891,6 +1891,44 @@ public void testDataverseDatasetCounts() throws InterruptedException {
                 .body("data.total_count", CoreMatchers.equalTo(1))
                 .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias3))
                 .body("data.items[0].datasetCount", CoreMatchers.equalTo(0));
+
+        // Check that datasets in child collections are counted
+        Response createDataverseResponse4 = UtilIT.createRandomDataverse(apiToken);
+        createDataverseResponse4.prettyPrint();
+        String dataverseAlias4 = UtilIT.getAliasFromResponse(createDataverseResponse4);
+
+        Response publishDataverse4 = UtilIT.publishDataverseViaNativeApi(dataverseAlias4, apiToken);
+        publishDataverse4.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        String childDataverseAlias = dataverseAlias4 + "-child";
+        Response createChildDataverseResponse = UtilIT.createSubDataverse(childDataverseAlias, null, apiToken, dataverseAlias4);
+        createChildDataverseResponse.prettyPrint();
+
+        Response publishChildDataverse = UtilIT.publishDataverseViaNativeApi(childDataverseAlias, apiToken);
+        publishChildDataverse.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        Response createGrandchildDatasetResponse = UtilIT.createRandomDatasetViaNativeApi(childDataverseAlias, apiToken);
+        createGrandchildDatasetResponse.prettyPrint();
+        String grandchildDatasetPid = JsonPath.from(createGrandchildDatasetResponse.getBody().asString()).getString("data.persistentId");
+
+        Response publishGrandchildDataset = UtilIT.publishDatasetViaNativeApi(grandchildDatasetPid, "major", apiToken);
+        publishGrandchildDataset.then().assertThat()
+                .statusCode(OK.getStatusCode());
+        UtilIT.sleepForReindex(grandchildDatasetPid, apiToken, 5);
+
+        // Wait for reindex of dataverse after publishing
+        String searchDataverseWithGrandchildDatasetQuery = "identifier:" + dataverseAlias4 + " AND datasetCount:1";
+        assertTrue(UtilIT.sleepForSearch(searchDataverseWithGrandchildDatasetQuery, null, "", 1, UtilIT.MAXIMUM_INGEST_LOCK_DURATION));
+
+        Response searchDataverseWithGrandchildDataset = UtilIT.search(searchDataverseWithGrandchildDatasetQuery, apiToken, "&type=dataverse");
+        searchDataverseWithGrandchildDataset.prettyPrint();
+        searchDataverseWithGrandchildDataset.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.total_count", CoreMatchers.equalTo(1))
+                .body("data.items[0].identifier", CoreMatchers.equalTo(dataverseAlias4))
+                .body("data.items[0].datasetCount", CoreMatchers.equalTo(1));
     }
 
     @AfterEach

From 88cff957bb086c03a64130e83839e9182e48118c Mon Sep 17 00:00:00 2001
From: Omer Fahim <mfahim11427@gmail.com>
Date: Thu, 7 Aug 2025 11:33:51 -0400
Subject: [PATCH 11/11] Update pom.xml

bumped version number
---
 modules/dataverse-parent/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/dataverse-parent/pom.xml b/modules/dataverse-parent/pom.xml
index df1b31181bd..44691820f4b 100644
--- a/modules/dataverse-parent/pom.xml
+++ b/modules/dataverse-parent/pom.xml
@@ -132,7 +132,7 @@
  
     <properties>
         <!-- This is a special Maven property name, do not change! -->
-        <revision>6.7</revision>
+        <revision>6.7.1</revision>
     
         <target.java.version>17</target.java.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>