4410 dataset linking

doc/sphinx-guides/source/admin/dataverses-datasets.rst

@@ -41,7 +41,7 @@ Moves a dataset whose id is passed to a dataverse whose alias is passed. If the
 Link a Dataset
 ^^^^^^^^^^^^^^
 
-Creates a link between a dataset and a dataverse (see the Linked Dataverses + Linked Datasets section of the :doc:`/user/dataverse-management` guide for more information). Only accessible to superusers. ::
+Creates a link between a dataset and a dataverse (see the Linked Dataverses + Linked Datasets section of the :doc:`/user/dataverse-management` guide for more information). ::
 
     curl -H "X-Dataverse-key: $API_TOKEN" -X PUT http://$SERVER/api/datasets/$linked-dataset-id/link/$linking-dataverse-alias
 

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

@@ -501,6 +501,13 @@ In the example below, the curator has saved the JSON file as :download:`reason-f
 
 The review process can sometimes resemble a tennis match, with the authors submitting and resubmitting the dataset over and over until the curators are satisfied. Each time the curators send a "reason for return" via API, that reason is persisted into the database, stored at the dataset version level.
 
+Link a Dataset
+~~~~~~~~~~~~~~
+
+Creates a link between a dataset and a dataverse (see the Linked Dataverses + Linked Datasets section of the :doc:`/user/dataverse-management` guide for more information). ::
+
+    curl -H "X-Dataverse-key: $API_TOKEN" -X PUT http://$SERVER/api/datasets/$linked-dataset-id/link/$linking-dataverse-alias
+
 Dataset Locks
 ~~~~~~~~~~~~~
 

doc/sphinx-guides/source/user/dataverse-management.rst

@@ -189,14 +189,26 @@ Click on Featured Dataverses and a pop up will appear. Select which sub datavers
 
 Note: Featured Dataverses can only be used with published dataverses.
 
-Linked Dataverses + Linked Datasets
-======================================================
+Dataset Linking
+===============
+
+Dataset linking allows a dataverse owner to "link" their dataverse to a dataset that exists outside of that dataverse, so it appears in the dataverse’s list of contents without actually *being* in that dataverse. You can link other users' datasets to your dataverse, but that does not transfer editing or other special permissions to you. The linked dataset will still be under the original user's control. 
+
+For example, researchers working on a collaborative study across institutions can each link their own individual institutional dataverses to the one collaborative dataset, making it easier for interested parties from each institution to find the study.
+
+In order to link a dataset, you will need your account to have the "Add Dataset" permission on the Dataverse that is doing the linking. If you created the dataverse then you should have this permission already, but if not then you will need to ask the admin of that dataverse to assign that permission to your account. You do not need any special permissions on the dataset being linked.
 
-Currently, the ability to link a dataverse to another dataverse or a dataset to a dataverse is a super user only feature. 
+To link a dataset to your dataverse, you must navigate to that dataset and click the white "Link" button in the upper-right corner of the dataset page. This will open up a window where you can type in the name of the dataverse that you would like to link the dataset to. Select your dataverse and click the save button. This will establish the link, and the dataset will now appear under your dataverse.
+
+There is currently no way to remove established links in the UI. If you need to remove a link between a dataverse and a dataset, please contact the support team for the Dataverse installation you are using.
+
+
+Dataverse Linking
+======================================================
 
-If you link a dataset to your dataverse, that means that the dataset will appear in the list of datasets contained within your dataverse. Linking another dataverse to your dataverse works the same way. You can link other users' dataverses and datasets to your dataverse, but that does not transfer editing or other special permissions to you. The linked dataverse or dataset will still be under the original user's control.
+Similarly to dataset linking, dataverse linking allows a dataverse owner to "link" their dataverse to another dataverse, so the dataverse being linked will appear in the linking dataverse's list of contents without actually *being* in that dataverse. Currently, the ability to link a dataverse to another dataverse is a superuser only feature. 
 
-If you need to have a dataverse or dataset linked to your dataverse, please contact the support team for the Dataverse installation you are using.
+If you need to have a dataverse linked to your dataverse, please contact the support team for the Dataverse installation you are using.
 
 Publish Your Dataverse
 =================================================================

src/main/java/Bundle.properties

@@ -684,11 +684,16 @@ dataverse.contact=Email Dataverse Contact
 dataset.link=Link Dataset
 dataverse.link=Link Dataverse
 dataverse.link.btn.tip=Link to Your Dataverse
-dataverse.link.yourDataverses=Your {0, choice, 1#Dataverse|2#Dataverses}
+dataverse.link.yourDataverses=Your Dataverse
+dataverse.link.yourDataverses.inputPlaceholder=Enter Dataverse Name
 dataverse.link.save=Save Linked Dataverse
 dataset.link.save=Save Linked Dataset
+dataset.link.not.to.owner=Can't link a dataset to its dataverse
+dataset.link.not.to.parent.dataverse=Can't link a dataset to its parent dataverses
+dataset.link.not.published=Can't link a dataset that has not been published
 dataverse.link.dataverse.choose=Choose which of your dataverses you would like to link this dataverse to.
-dataverse.link.dataset.choose=Choose which of your dataverses you would like to link this dataset to.
+dataverse.link.dataset.choose=Enter the name of the dataverse you would like to link this dataset to. If you need to remove this link in the future, please contact {0}.
+dataverse.link.dataset.none=No linkable dataverses available.
 dataverse.link.no.choice=You have one dataverse you can add linked dataverses and datasets in.
 dataverse.link.no.linkable=To be able to link a dataverse or dataset, you need to have your own dataverse. Click on the Add Data button on the homepage to get started.
 dataverse.link.no.linkable.remaining=You have already linked all of your eligible dataverses.
@@ -1909,6 +1914,7 @@ dataverse.edit.msg=Edit Dataverse
 dataverse.edit.detailmsg= - Edit your dataverse and click Save. Asterisks indicate required fields.
 dataverse.feature.update=The featured dataverses for this dataverse have been updated.
 dataverse.link.select=You must select a linking dataverse.
+dataset.noSelectedDataverse.header=Select Dataverse(s)
 dataverse.link.user=Only authenticated users can link a dataverse.
 dataverse.link.error=Unable to link {0} to {1}. An internal error occurred.
 dataverse.search.user=Only authenticated users can save a search.

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

@@ -93,6 +93,7 @@
 import edu.harvard.iq.dataverse.externaltools.ExternalToolServiceBean;
 import edu.harvard.iq.dataverse.export.SchemaDotOrgExporter;
 import java.util.Collections;
+import javax.faces.component.UIInput;
 
 import javax.faces.event.AjaxBehaviorEvent;
 import javax.servlet.ServletOutputStream;
@@ -238,7 +239,6 @@ public enum DisplayMode {
 
     private boolean stateChanged = false;
 
-    private List<Dataverse> dataversesForLinking = new ArrayList<>();
     private Long linkingDataverseId;
     private List<SelectItem> linkingDVSelectItems;
     private Dataverse linkingDataverse;
@@ -738,59 +738,14 @@ public void setLinkingDataverseId(Long linkingDataverseId) {
         this.linkingDataverseId = linkingDataverseId;
     }
 
-    public List<Dataverse> getDataversesForLinking() {
-        return dataversesForLinking;
-    }
 
-    public void setDataversesForLinking(List<Dataverse> dataversesForLinking) {
-        this.dataversesForLinking = dataversesForLinking;
-    }
 
     public void updateReleasedVersions(){
 
         setReleasedVersionTabList(resetReleasedVersionTabList());
 
     }
 
-    public void updateLinkableDataverses() {
-        dataversesForLinking = new ArrayList<>();
-        linkingDVSelectItems = new ArrayList<>();
-
-        //Since this is a super user we are getting all dataverses
-        dataversesForLinking = dataverseService.findAll();
-        if (dataversesForLinking.isEmpty()) {
-            setNoDVsAtAll(true);
-            return;
-        }
-
-        dataversesForLinking.remove(dataset.getOwner());
-        Dataverse testDV = dataset.getOwner();
-        while(testDV.getOwner() != null){
-            dataversesForLinking.remove(testDV.getOwner());
-            testDV = testDV.getOwner();
-        }                      
-
-        for (Dataverse removeLinked : dsLinkingService.findLinkingDataverses(dataset.getId())) {
-            dataversesForLinking.remove(removeLinked);
-        }
-        for (Dataverse removeLinked : dvLinkingService.findLinkingDataverses(dataset.getOwner().getId())) {
-            dataversesForLinking.remove(removeLinked);
-        }
-
-        if (dataversesForLinking.isEmpty()) {
-            setNoDVsRemaining(true);            
-            return;
-        }
-
-        for (Dataverse selectDV : dataversesForLinking) {
-            linkingDVSelectItems.add(new SelectItem(selectDV.getId(), selectDV.getDisplayName()));
-        }
-
-        if (!dataversesForLinking.isEmpty() && dataversesForLinking.size() == 1 && dataversesForLinking.get(0) != null) {
-            linkingDataverse = dataversesForLinking.get(0);
-            linkingDataverseId = linkingDataverse.getId();
-        }
-    }
 
     public void updateSelectedLinkingDV(ValueChangeEvent event) {
         linkingDataverseId = (Long) event.getNewValue();
@@ -2128,6 +2083,16 @@ public void setSelectedFiles(List<FileMetadata> selectedFiles) {
         this.selectedFiles = selectedFiles;
     }
 
+    private Dataverse selectedDataverseForLinking;
+
+    public Dataverse getSelectedDataverseForLinking() {
+        return selectedDataverseForLinking;
+    }
+
+    public void setSelectedDataverseForLinking(Dataverse sdvfl) {
+        this.selectedDataverseForLinking = sdvfl;
+    }
+
     private List<FileMetadata> selectedRestrictedFiles; // = new ArrayList<>();
 
     public List<FileMetadata> getSelectedRestrictedFiles() {
@@ -2294,37 +2259,83 @@ public void updateFileCounts(){
 
     private List<String> getSuccessMessageArguments() {
         List<String> arguments = new ArrayList<>();
+        String dataverseString = "";
         arguments.add(StringEscapeUtils.escapeHtml(dataset.getDisplayName()));
-        String linkString = "<a href=\"/dataverse/" + linkingDataverse.getAlias() + "\">" + StringEscapeUtils.escapeHtml(linkingDataverse.getDisplayName()) + "</a>";
-        arguments.add(linkString);
+        dataverseString += " <a href=\"/dataverse/" + selectedDataverseForLinking.getAlias() + "\">" + StringEscapeUtils.escapeHtml(selectedDataverseForLinking.getDisplayName()) + "</a>";
+        arguments.add(dataverseString);
         return arguments;
     }
 
-    public String saveLinkedDataset() {
-        if (linkingDataverseId == null) {
-            JsfHelper.addFlashMessage(BundleUtil.getStringFromBundle("dataverse.link.select"));
-            return "";
+
+    public void saveLinkingDataverses() {
+
+        if (selectedDataverseForLinking == null) {
+            FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "", BundleUtil.getStringFromBundle("dataverse.link.select"));
+            FacesContext.getCurrentInstance().addMessage(null, message);
+            return;
+        }     
+
+        if(saveLink(selectedDataverseForLinking)){
+            JsfHelper.addSuccessMessage(BundleUtil.getStringFromBundle("dataset.message.linkSuccess", getSuccessMessageArguments()));
+        } else{           
+            FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.notlinked"), linkingDataverseErrorMessage);
+            FacesContext.getCurrentInstance().addMessage(null, message);
         }
-        linkingDataverse = dataverseService.find(linkingDataverseId);
+    } 
+
+    private String linkingDataverseErrorMessage = "";
+
+
+    public String getLinkingDataverseErrorMessage() {
+        return linkingDataverseErrorMessage;
+    }
+
+    public void setLinkingDataverseErrorMessage(String linkingDataverseErrorMessage) {
+        this.linkingDataverseErrorMessage = linkingDataverseErrorMessage;
+    }
+
+    UIInput selectedLinkingDataverseMenu;
+
+    public UIInput getSelectedDataverseMenu() {
+        return selectedLinkingDataverseMenu;
+    }
+
+    public void setSelectedDataverseMenu(UIInput selectedDataverseMenu) {
+        this.selectedLinkingDataverseMenu = selectedDataverseMenu;
+    }
+
+
+    private Boolean saveLink(Dataverse dataverse){
+        boolean retVal = true;
         if (readOnly) {
             // Pass a "real", non-readonly dataset the the LinkDatasetCommand: 
             dataset = datasetService.find(dataset.getId());
         }
-        LinkDatasetCommand cmd = new LinkDatasetCommand(dvRequestService.getDataverseRequest(), linkingDataverse, dataset);
+        LinkDatasetCommand cmd = new LinkDatasetCommand(dvRequestService.getDataverseRequest(), dataverse, dataset);
+        linkingDataverse = dataverse;
         try {
-            commandEngine.submit(cmd);
-            JsfHelper.addSuccessMessage(BundleUtil.getStringFromBundle("dataset.message.linkSuccess", getSuccessMessageArguments()));
+            commandEngine.submit(cmd);           
         } catch (CommandException ex) {
             String msg = "There was a problem linking this dataset to yours: " + ex;
             logger.severe(msg);
             msg = BundleUtil.getStringFromBundle("dataset.notlinked.msg") + ex;
             /**
              * @todo how do we get this message to show up in the GUI?
              */
-            FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.notlinked"), msg);
-            FacesContext.getCurrentInstance().addMessage(null, message);
+            linkingDataverseErrorMessage = msg;
+            retVal = false;
+        }
+        return retVal;
+    }
+
+
+    public List<Dataverse> completeLinkingDataverse(String query) {
+        dataset = datasetService.find(dataset.getId());
+        if (session.getUser().isAuthenticated()) {
+            return dataverseService.filterDataversesForLinking(query, dvRequestService.getDataverseRequest(), dataset);
+        } else {
+            return null;
         }
-        return returnToLatestVersion();
     }
 
     List<FileMetadata> previouslyRestrictedFiles = null;

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

@@ -44,7 +44,8 @@
     @NamedQuery(name = "Dataverse.findRoot", query = "SELECT d FROM Dataverse d where d.owner.id=null"),
     @NamedQuery(name = "Dataverse.findByAlias", query="SELECT dv FROM Dataverse dv WHERE LOWER(dv.alias)=:alias"),
     @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.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")
 })
 @Entity
 @Table(indexes = {@Index(columnList="defaultcontributorrole_id")

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

@@ -5,8 +5,11 @@
  */
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.authorization.Permission;
+import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
 import edu.harvard.iq.dataverse.authorization.users.User;
 import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
+import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import edu.harvard.iq.dataverse.search.SolrSearchResult;
 import edu.harvard.iq.dataverse.util.SystemConfig;
@@ -49,13 +52,16 @@ public class DataverseServiceBean implements java.io.Serializable {
 
     @EJB
     DatasetServiceBean datasetService;
-
+    
     @EJB
     DataverseLinkingServiceBean dataverseLinkingService;
 
     @EJB
     DatasetLinkingServiceBean datasetLinkingService;
 
+    @EJB
+    PermissionServiceBean permissionService;
+
     @EJB
     SystemConfig systemConfig;
 
@@ -179,7 +185,7 @@ public Dataverse findByAlias(String anAlias) {
             return null;
         }
     }
-	
+    
 	public boolean hasData( Dataverse dv ) {
 		TypedQuery<Long> amountQry = em.createNamedQuery("Dataverse.ownedObjectsById", Long.class)
 								.setParameter("id", dv.getId());
@@ -441,6 +447,34 @@ public List<Dataverse> filterByAliasQuery(String filterQuery) {
         return ret;
     }
 
+    public List<Dataverse> filterDataversesForLinking(String query, DataverseRequest req, Dataset dataset) {
+
+        List<Dataverse> dataverseList = new ArrayList<>();
+
+        List<Dataverse> results = em.createNamedQuery("Dataverse.filterByName", Dataverse.class)
+                .setParameter("name", "%" + query.toLowerCase() + "%")
+                .getResultList();
+
+        List<Object> alreadyLinkeddv_ids = em.createNativeQuery("SELECT linkingdataverse_id   FROM datasetlinkingdataverse WHERE dataset_id = " + dataset.getId()).getResultList();
+        List<Dataverse> remove = new ArrayList<>();
+
+        if (alreadyLinkeddv_ids != null && !alreadyLinkeddv_ids.isEmpty()) {
+            alreadyLinkeddv_ids.stream().map((testDVId) -> this.find(testDVId)).forEachOrdered((removeIt) -> {
+                remove.add(removeIt);
+            });
+        }
+
+        for (Dataverse res : results) {
+            if (!remove.contains(res)) {
+                if (this.permissionService.requestOn(req, res).has(Permission.PublishDataset)) {
+                    dataverseList.add(res);
+                }
+            }
+        }
+
+        return dataverseList;
+    }
+
     /**
      * Used to identify and properly display Harvested objects on the dataverse page.
      * 

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

@@ -159,6 +159,12 @@ public String getSupportTeamName() {
         InternetAddress systemAddress = MailUtil.parseSystemAddress(systemEmail);
         return BrandingUtil.getSupportTeamName(systemAddress, dataverseService.findRootDataverse().getName());
     }
+
+    public String getSupportTeamEmail() {
+        String systemEmail = getValueForKey(SettingsServiceBean.Key.SystemEmail);
+        InternetAddress systemAddress = MailUtil.parseSystemAddress(systemEmail);        
+        return BrandingUtil.getSupportTeamEmailAddress(systemAddress) != null ? BrandingUtil.getSupportTeamEmailAddress(systemAddress) : BrandingUtil.getSupportTeamName(systemAddress, dataverseService.findRootDataverse().getName());
+    }
 
     public boolean isRootDataverseThemeDisabled() {
         return isTrueForKey(Key.DisableRootDataverseTheme, false);

src/main/java/edu/harvard/iq/dataverse/authorization/Permission.java

@@ -47,7 +47,7 @@ public enum Permission implements java.io.Serializable {
     ManageDataversePermissions(BundleUtil.getStringFromBundle("permission.managePermissionsDataverse"), true, Dataverse.class),
     ManageDatasetPermissions(BundleUtil.getStringFromBundle("permission.managePermissionsDataset"), true, Dataset.class),
     PublishDataverse(BundleUtil.getStringFromBundle("permission.publishDataverse"), true, Dataverse.class),
-    PublishDataset(BundleUtil.getStringFromBundle("permission.publishDataset"), true, Dataset.class),
+    PublishDataset(BundleUtil.getStringFromBundle("permission.publishDataset"), true, Dataset.class, Dataverse.class),
     // Delete
     DeleteDataverse(BundleUtil.getStringFromBundle("permission.deleteDataverse"), true, Dataverse.class),
     DeleteDatasetDraft(BundleUtil.getStringFromBundle("permission.deleteDataset"), true, Dataset.class);