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Merge pull request #11741 from IQSS/11710-find-dataverses-for-linking
11710 find dataverses for linking
2 parents 94fa2fb + 0982ff2 commit 6c17c9d

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‎doc/release-notes/11710-get-available-dataverses-api.md‎

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### New API endpoint for retrieving a list of Dataverse Collections to which a given Dataset or Dataverse Collection may be linked
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-The end point also takes in a search term which currently must be part of the collections' names.
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-The user calling this API must have Link Dataset or Link Dataverse permission on the Dataverse Collections returned.
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-If the Collection has already been linked to the given Dataset or Collection, it will not be returned.

‎doc/sphinx-guides/source/api/native-api.rst‎

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@@ -732,6 +732,50 @@ Note: you must have "Add Dataset" permission in the given collection to invoke t
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.. _featured-collections:
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List Dataverse Collections to Which a Given Dataset or Dataverse Collection May Be Linked
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The user may provide a search term to limit the list of Dataverse Collections returned. The search term will be compared to the name of the Dataverse Collections.
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The response is a JSON array of the ids, aliases, and names of the Dataverse collections to which a given Dataset or Dataverse Collection may be linked:
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For a given Dataverse Collection:
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.. code-block:: bash
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export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
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export SERVER_URL=https://demo.dataverse.org
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export OBJECT_TYPE=dataverse
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export ID=collectionAlias
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export SEARCH_TERM=searchOn
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curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER_URL/api/dataverses/$ID/$OBJECT_TYPE/linkingDataverses?searchTerm=$SEARCH_TERM"
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The fully expanded example above (without environment variables) looks like this:
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.. code-block:: bash
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curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X GET "https://demo.dataverse.org/api/dataverses/collectionAlias/dataverse/linkingDataverses?searchTerm=searchOn"
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For a given Dataset:
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.. code-block:: bash
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export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
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export SERVER_URL=https://demo.dataverse.org
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export OBJECT_TYPE=dataset
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export PERSISTENT_IDENTIFIER=doi:10.5072/FK2/J8SJZB
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export SEARCH_TERM=searchOn
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curl -H "X-Dataverse-key:$API_TOKEN" -X GET "$SERVER_URL/api/dataverses/:persistentId/$OBJECT_TYPE/linkingDataverses?searchTerm=SEARCH_TERM&persistentId=$PERSISTENT_IDENTIFIER"
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The fully expanded example above (without environment variables) looks like this:
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.. code-block:: bash
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curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X GET "https://demo.dataverse.org/api/dataverses/:persistentId/dataset/linkingDataverses?searchTerm=searchOn&persistentId=doi:10.5072/FK2/J8SJZB"
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You may also add an optional "alreadyLinked=true" parameter to return collections which are already linked to the given Dataset or Dataverse Collection.
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List Featured Collections for a Dataverse Collection
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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‎src/main/java/edu/harvard/iq/dataverse/DatasetLinkingDataverse.java‎

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import jakarta.persistence.Id;
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import jakarta.persistence.Index;
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import jakarta.persistence.JoinColumn;
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import jakarta.persistence.NamedNativeQuery;
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import jakarta.persistence.NamedQueries;
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import jakarta.persistence.NamedQuery;
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import jakarta.persistence.OneToOne;
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@NamedQuery(name = "DatasetLinkingDataverse.findIdsByLinkingDataverseId",
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query = "SELECT o.dataset.id FROM DatasetLinkingDataverse AS o WHERE o.linkingDataverse.id = :linkingDataverseId")
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})
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@NamedNativeQuery(
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name = "DatasetLinkingDataverse.findByDatasetIdAndLinkingDataverseName",
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query = """
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select o.linkingDataverse_id from DatasetLinkingDataverse as o
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LEFT JOIN dataverse dv ON dv.id = o.linkingDataverse_id
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WHERE o.dataset_id =? AND ((LOWER(dv.name) LIKE ? and ((SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?)
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or (SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?)))
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or (LOWER(dv.name) NOT LIKE ? and ((LOWER(dv.name) LIKE ?)
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or (LOWER(dv.name) LIKE ?))))"""
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)
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public class DatasetLinkingDataverse implements Serializable {
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private static final long serialVersionUID = 1L;
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@Id

‎src/main/java/edu/harvard/iq/dataverse/DatasetLinkingServiceBean.java‎

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*/
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package edu.harvard.iq.dataverse;
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import jakarta.ejb.EJB;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.logging.Logger;
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import jakarta.persistence.EntityManager;
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import jakarta.persistence.NoResultException;
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import jakarta.persistence.PersistenceContext;
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import jakarta.persistence.Query;
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import jakarta.persistence.TypedQuery;
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/**
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@PersistenceContext(unitName = "VDCNet-ejbPU")
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private EntityManager em;
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@EJB
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DataverseServiceBean dataverseService;
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public List<Dataset> findLinkedDatasets(Long dataverseId) {
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}
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public List<Dataverse> findLinkingDataverses(Long datasetId) {
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return findLinkingDataverses(datasetId, "");
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}
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public List<Dataverse> findLinkingDataverses(Long datasetId, String searchTerm) {
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List<Dataverse> retList = new ArrayList<>();
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TypedQuery<DatasetLinkingDataverse> typedQuery = em.createNamedQuery("DatasetLinkingDataverse.findByDatasetId", DatasetLinkingDataverse.class)
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.setParameter("datasetId", datasetId);
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for (DatasetLinkingDataverse datasetLinkingDataverse : typedQuery.getResultList()) {
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retList.add(datasetLinkingDataverse.getLinkingDataverse());
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if (searchTerm == null || searchTerm.isEmpty()) {
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TypedQuery<DatasetLinkingDataverse> typedQuery = em.createNamedQuery("DatasetLinkingDataverse.findByDatasetId", DatasetLinkingDataverse.class)
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.setParameter("datasetId", datasetId);
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for (DatasetLinkingDataverse datasetLinkingDataverse : typedQuery.getResultList()) {
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retList.add(datasetLinkingDataverse.getLinkingDataverse());
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}
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return retList;
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} else {
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String pattern = searchTerm.toLowerCase();
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String pattern1 = pattern + "%";
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String pattern2 = "% " + pattern + "%";
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// Adjust the queries for very short, 1 and 2-character patterns:
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if (pattern.length() == 1) {
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pattern1 = pattern;
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pattern2 = pattern + " %";
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}
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TypedQuery<Long> typedQuery
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= em.createNamedQuery("DatasetLinkingDataverse.findByDatasetIdAndLinkingDataverseName", Long.class)
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.setParameter(1, datasetId).setParameter(2, "%dataverse").setParameter(3, pattern1)
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.setParameter(4, pattern2).setParameter(5, "%dataverse").setParameter(6, pattern1).setParameter(7, pattern2);
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for (Long id : typedQuery.getResultList()) {
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retList.add(dataverseService.find(id));
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}
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return retList;
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}
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return retList;
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}
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public void save(DatasetLinkingDataverse datasetLinkingDataverse) {

‎src/main/java/edu/harvard/iq/dataverse/DataverseLinkingDataverse.java‎

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import jakarta.persistence.Id;
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import jakarta.persistence.Index;
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import jakarta.persistence.JoinColumn;
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import jakarta.persistence.NamedNativeQuery;
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import jakarta.persistence.NamedQueries;
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import jakarta.persistence.NamedQuery;
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import jakarta.persistence.OneToOne;
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@NamedQuery(name = "DataverseLinkingDataverse.findIdsByLinkingDataverseId",
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query = "SELECT o.dataverse.id FROM DataverseLinkingDataverse AS o WHERE o.linkingDataverse.id = :linkingDataverseId")
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})
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@NamedNativeQuery(
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name = "DataverseLinkingDataverse.findByDataverseIdAndLinkingDataverseName",
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query = """
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select o.linkingDataverse_id from DataverseLinkingDataverse as o
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LEFT JOIN dataverse dv ON dv.id = o.linkingDataverse_id
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WHERE o.dataverse_id =? AND ((LOWER(dv.name) LIKE ? and ((SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?)
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or (SUBSTRING(LOWER(dv.name),0,(LENGTH(dv.name)-9)) LIKE ?)))
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or (LOWER(dv.name) NOT LIKE ? and ((LOWER(dv.name) LIKE ?)
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or (LOWER(dv.name) LIKE ?))))"""
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)
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public class DataverseLinkingDataverse implements Serializable {
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private static final long serialVersionUID = 1L;
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@Id

‎src/main/java/edu/harvard/iq/dataverse/DataverseLinkingServiceBean.java‎

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@@ -43,12 +43,41 @@ public List<Dataverse> findLinkedDataverses(Long linkingDataverseId) {
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}
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public List<Dataverse> findLinkingDataverses(Long dataverseId) {
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return findLinkingDataverses(dataverseId, "");
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}
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public List<Dataverse> findLinkingDataverses(Long dataverseId, String searchTerm) {
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List<Dataverse> retList = new ArrayList<>();
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TypedQuery<DataverseLinkingDataverse> typedQuery = em.createNamedQuery("DataverseLinkingDataverse.findByDataverseId", DataverseLinkingDataverse.class)
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.setParameter("dataverseId", dataverseId);
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for (DataverseLinkingDataverse dataverseLinkingDataverse : typedQuery.getResultList()) {
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retList.add(dataverseLinkingDataverse.getLinkingDataverse());
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if (searchTerm == null || searchTerm.isEmpty()) {
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TypedQuery<DataverseLinkingDataverse> typedQuery = em.createNamedQuery("DataverseLinkingDataverse.findByDataverseId", DataverseLinkingDataverse.class)
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.setParameter("dataverseId", dataverseId);
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for (DataverseLinkingDataverse dataverseLinkingDataverse : typedQuery.getResultList()) {
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retList.add(dataverseLinkingDataverse.getLinkingDataverse());
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}
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} else {
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String pattern = searchTerm.toLowerCase();
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String pattern1 = pattern + "%";
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String pattern2 = "% " + pattern + "%";
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// Adjust the queries for very short, 1 and 2-character patterns:
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if (pattern.length() == 1) {
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pattern1 = pattern;
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pattern2 = pattern + " %";
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}
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TypedQuery<Long> typedQuery
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= em.createNamedQuery("DataverseLinkingDataverse.findByDataverseIdAndLinkingDataverseName", Long.class)
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.setParameter(1, dataverseId).setParameter(2, "%dataverse").setParameter(3, pattern1)
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.setParameter(4, pattern2).setParameter(5, "%dataverse").setParameter(6, pattern1).setParameter(7, pattern2);
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for (Long id : typedQuery.getResultList()) {
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retList.add(dataverseService.find(id));
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}
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}
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return retList;
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}
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‎src/main/java/edu/harvard/iq/dataverse/DataverseServiceBean.java‎

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return ret;
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}
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public List<Dataverse> filterDataversesForLinking(String query, DataverseRequest req, Dataset dataset) {
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public List<Dataverse> filterDataversesForLinking(String query, DataverseRequest req, DvObject dvo) {
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List<Dataverse> dataverseList = new ArrayList<>();
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List<Dataverse> results = filterDataversesByNamePattern(query);
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if (results == null || results.size() == 0) {
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return null;
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if (results == null || results.isEmpty()) {
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return null;
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}
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Dataset linkedDataset = null;
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Dataverse linkedDataverse = null;
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List<Object> alreadyLinkeddv_ids;
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if ((dvo instanceof Dataset)) {
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linkedDataset = (Dataset) dvo;
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alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id FROM datasetlinkingdataverse WHERE dataset_id = " + linkedDataset.getId()).getResultList();
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} else {
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linkedDataverse = (Dataverse) dvo;
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alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id FROM dataverselinkingdataverse WHERE dataverse_id = " + linkedDataverse.getId()).getResultList();
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}
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List<Object> alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id FROM datasetlinkingdataverse WHERE dataset_id = " + dataset.getId()).getResultList();
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List<Dataverse> remove = new ArrayList<>();
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if (alreadyLinkeddv_ids != null && !alreadyLinkeddv_ids.isEmpty()) {
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alreadyLinkeddv_ids.stream().map((testDVId) -> this.find(testDVId)).forEachOrdered((removeIt) -> {
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remove.add(removeIt);
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});
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}
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if (dvo instanceof Dataverse dataverse) {
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remove.add(dataverse);
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}
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for (Dataverse res : results) {
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if (!remove.contains(res)) {
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if (this.permissionService.requestOn(req, res).has(Permission.LinkDataset)) {
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if ((linkedDataset != null && this.permissionService.requestOn(req, res).has(Permission.LinkDataset))
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|| (linkedDataverse != null && this.permissionService.requestOn(req, res).has(Permission.LinkDataverse))) {
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dataverseList.add(res);
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}
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}
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}
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return dataverseList;
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}
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public List<Dataverse> removeUnlinkableDataverses(List<Dataverse> allWithPerms, DvObject dvo) {
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List<Dataverse> dataverseList = new ArrayList<>();
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Dataset linkedDataset = null;
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Dataverse linkedDataverse = null;
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List<Object> alreadyLinkeddv_ids;
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if ((dvo instanceof Dataset)) {
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linkedDataset = (Dataset) dvo;
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alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id FROM datasetlinkingdataverse WHERE dataset_id = " + linkedDataset.getId()).getResultList();
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} else {
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linkedDataverse = (Dataverse) dvo;
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alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id FROM dataverselinkingdataverse WHERE dataverse_id = " + linkedDataverse.getId()).getResultList();
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}
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List<Dataverse> remove = new ArrayList<>();
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if (alreadyLinkeddv_ids != null && !alreadyLinkeddv_ids.isEmpty()) {
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alreadyLinkeddv_ids.stream().map((testDVId) -> this.find(testDVId)).forEachOrdered((removeIt) -> {
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remove.add(removeIt);
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});
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}
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if (dvo instanceof Dataverse dataverse) {
578+
remove.add(dataverse);
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}
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DvObject testDVO = dvo;
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//Remove DVO's parent up to Root
583+
while (testDVO != null) {
584+
if (testDVO.getOwner() == null) {
585+
break; // we are at the root; which by definition is metadata block root, regardless of the value
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}
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remove.add((Dataverse) testDVO.getOwner());
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testDVO = testDVO.getOwner();
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}
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for (Dataverse res : allWithPerms) {
592+
if (!remove.contains(res)) {
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dataverseList.add(res);
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}
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}
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return dataverseList;
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}
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public List<Dataverse> filterDataversesForUnLinking(String query, DataverseRequest req, Dataset dataset) {
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List<Object> alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id FROM datasetlinkingdataverse WHERE dataset_id = " + dataset.getId()).getResultList();
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List<Dataverse> dataverseList = new ArrayList<>();

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