Merge pull request #8706 from IQSS/8600-duplicate-template

8600 duplicate template

doc/release-notes/8600-duplicate-templates.md

@@ -0,0 +1,9 @@
+###Duplicate Templates in Database
+Prior to this release making a copy of a Dataset Template was creating two copies, one of which is visible in the dataverse, the other not being assigned 
+a dataverse was invisible to the user (https://github.com/IQSS/dataverse/issues/8600). This release fixes the issue. 
+
+If you would like to remove these orphan templates you may run the follwing script:
+
+https://github.com/IQSS/dataverse/raw/develop/scripts/issues/8600/delete_orphan_templates_8600.sh
+
+Also, admin APIs for finding and deleting templates have been added.

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

@@ -3806,3 +3806,36 @@ Superusers can delete a license that is not in use by the license ``$ID``:
 .. code-block:: bash
 
   curl -X DELETE -H X-Dataverse-key:$API_TOKEN $SERVER_URL/api/licenses/$ID
+  
+List Dataset Templates
+~~~~~~~~~~~~~~~~~~~~~~
+
+List all templates in the system. ::
+
+    GET http://$SERVER/api/admin/templates
+    
+List templates in a given dataverse by the dataverse's alias or id. ::
+
+    GET http://$SERVER/api/admin/templates/{alias or id}
+
+    
+Delete Dataset Template
+~~~~~~~~~~~~~~~~~~~~~~~
+
+A curl example using an ``ID``
+
+.. code-block:: bash
+
+  export SERVER_URL=https://demo.dataverse.org
+  export ID=24
+
+  curl -X DELETE $SERVER_URL/api/admin/template/$ID
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -X DELETE https://demo.dataverse.org/api/admin/template/24
+  
+  
+  

scripts/issues/8600/delete_orphan_templates_8600.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+
+# begin config
+# PostgresQL credentials:
+# edit the following lines so that psql can talk to your database
+pg_host=localhost
+pg_port=5432
+pg_user=dvnapp
+pg_db=dvndb
+#edit this line with the server for the api call to delete orphan templates
+SERVER=http://localhost:8080/api
+# you can leave the password blank, if Postgres is configured 
+# to accept connections without auth:
+pg_pass=
+# psql executable - add full path, if necessary:
+PSQL_EXEC=psql
+
+# end config
+
+# check for orphan template : 
+
+PG_QUERY_0="SELECT count(t.id) FROM template t WHERE dataverse_id is null;"
+PG_QUERY_1="SELECT t.id, ',' FROM template t WHERE dataverse_id is null;"
+
+PGPASSWORD=$pg_pass; export PGPASSWORD
+
+echo "Checking the total number of orphan templates in database..."
+
+NUM_TEMPLATES=`${PSQL_EXEC} -h ${pg_host} -U ${pg_user} -d ${pg_db} -tA -F ' ' -c "${PG_QUERY_0}"`
+if [ $? != 0 ]
+then
+    echo "FAILED to execute psql! Check the credentials and try again?"
+    echo "exiting..."
+    echo 
+    echo "the command line that failed:"
+    echo "${PSQL_EXEC} -h ${pg_host} -U ${pg_user} -d ${pg_db} -tA -F ' ' -c \"${PG_QUERY_0}\""
+    exit 1
+fi
+
+echo $NUM_TEMPLATES total.
+echo 
+
+
+TEMPLATE_ID=`${PSQL_EXEC} -h ${pg_host} -U ${pg_user} -d ${pg_db} -tA -F ' ' -c "${PG_QUERY_1}"`
+
+echo $TEMPLATE_ID  to remove.
+
+
+${PSQL_EXEC}  -h ${pg_host} -U ${pg_user} -d ${pg_db} -t -c "${PG_QUERY_1}" \
+    -t \
+    --field-separator ' ' \
+    --quiet \
+| while read -a Record ; do
+    id=${Record[0]}
+
+	if [[ "x${id}" = "x" ]]
+	then
+		echo "nothing to do here"
+        else
+            curl -X DELETE $SERVER/admin/template/${id}
+            echo "template ${id} deleted "	
+        fi
+
+done
+
+NUM_TEMPLATES=`${PSQL_EXEC} -h ${pg_host} -U ${pg_user} -d ${pg_db} -tA -F ' ' -c "${PG_QUERY_0}"`
+
+echo $NUM_TEMPLATES orphan templates remaining.
+
+

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

@@ -118,15 +118,17 @@ public String cloneTemplate(Template templateIn) {
         newOne.setName(name);
         newOne.setUsageCount(new Long(0));
         newOne.setCreateTime(new Timestamp(new Date().getTime()));
-        dataverse.getTemplates().add(newOne);
-        templates.add(newOne);
+        newOne.setDataverse(dataverse);
+
         Template created;
         try {
             created = engineService.submit(new CreateTemplateCommand(newOne, dvRequestService.getDataverseRequest(), dataverse));
+            dataverse.getTemplates().add(created);
+            templates.add(created);
             saveDataverse("");
             String msg =  BundleUtil.getStringFromBundle("template.clone");//"The template has been copied";
             JsfHelper.addFlashMessage(msg);
-            return "/template.xhtml?id=" + created.getId() + "&ownerId=" + dataverse.getId() + "&editMode=METADATA&faces-redirect=true";
+            return "/template.xhtml?id=" + created.getId() + "&ownerId=" + dataverse.getId() + "&editMode=CLONE&faces-redirect=true";
         } catch (CommandException ex) {
             JH.addMessage(FacesMessage.SEVERITY_FATAL, BundleUtil.getStringFromBundle("template.clone.error"));//"Template could not be copied. " 
         }

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

@@ -28,12 +28,22 @@
 import javax.validation.constraints.Size;
 
 import edu.harvard.iq.dataverse.util.DateUtil;
+import javax.persistence.NamedQueries;
+import javax.persistence.NamedQuery;
 import org.hibernate.validator.constraints.NotBlank;
 
 /**
  *
  * @author skraffmiller
  */
+
+@NamedQueries({
+    @NamedQuery(name = "Template.findByOwnerId",
+               query = "select object(o) from Template as o where o.dataverse.id =:ownerId"),
+    @NamedQuery(name = "Template.findAll",
+               query = "select object(o) from Template as o")
+})
+
 @Entity
 @Table(indexes = {@Index(columnList="dataverse_id")})
 public class Template implements Serializable {

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

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.engine.command.Command;
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import edu.harvard.iq.dataverse.engine.command.impl.CreateTemplateCommand;
+import edu.harvard.iq.dataverse.engine.command.impl.DeleteTemplateCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.UpdateDataverseTemplateCommand;
 import edu.harvard.iq.dataverse.license.LicenseServiceBean;
@@ -12,6 +13,7 @@
 import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
 import java.sql.Timestamp;
 import java.util.Date;
+import java.util.List;
 import javax.ejb.EJB;
 import javax.ejb.EJBException;
 import javax.faces.application.FacesMessage;
@@ -53,7 +55,7 @@ public class TemplatePage implements java.io.Serializable {
 
     public enum EditMode {
 
-        CREATE, METADATA, LICENSE, LICENSEADD
+        CREATE, METADATA, LICENSE, LICENSEADD, CLONE
     };
 
     private Template template;
@@ -236,5 +238,20 @@ public String save(String redirectPage) {
     public void cancel() {
         editMode = null;
     }
+
+    public String deleteTemplate(Long templateId) {
+        List <Dataverse> dataverseWDefaultTemplate = null;
+        Template doomed = templateService.find(templateId);
+        dataverse.getTemplates().remove(doomed);  
+        dataverseWDefaultTemplate = templateService.findDataversesByDefaultTemplateId(doomed.getId());
+        try {
+            commandEngine.submit(new DeleteTemplateCommand(dvRequestService.getDataverseRequest(), getDataverse(), doomed, dataverseWDefaultTemplate  ));
+            JsfHelper.addFlashMessage(BundleUtil.getStringFromBundle("template.delete"));//("The template has been deleted");
+        } catch (CommandException ex) {
+            String failMessage = BundleUtil.getStringFromBundle("template.delete.error");//"The dataset template cannot be deleted.";
+            JH.addMessage(FacesMessage.SEVERITY_FATAL, failMessage);
+        }
+        return "/manage-templates.xhtml?dataverseId=" + dataverse.getId() + "&faces-redirect=true"; 
+    }
 
 }

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

@@ -31,22 +31,17 @@ public Template find(Object pk) {
     }
 
     public Template save(Template template) {
-        /*
-                if (template.getId() == null) {
-            em.persist(template);
-            return template;
-        } else {
-            return em.merge(template);
-        } */
         return em.merge(template);
     }
-
-    public Template findByDeafultTemplateOwnerId(Long ownerId) {
-        TypedQuery<Template> query = em.createQuery("select object(o.defaultTemplate) from Dataverse as o where o.owner.id =:ownerId order by o.name", Template.class);
-        query.setParameter("ownerId", ownerId);
-        return query.getSingleResult();
+
+    public List<Template> findByOwnerId(Long ownerId) {              
+        return em.createNamedQuery("Template.findByOwnerId", Template.class).setParameter("ownerId", ownerId).getResultList();
     }
-
+
+    public List<Template> findAll() {
+        return em.createNamedQuery("Template.findAll", Template.class).getResultList();
+    }
+
     public List<Dataverse> findDataversesByDefaultTemplateId(Long defaultTemplateId) {
         TypedQuery<Dataverse> query = em.createQuery("select object(o) from Dataverse as o where o.defaultTemplate.id =:defaultTemplateId order by o.name", Dataverse.class);
         query.setParameter("defaultTemplateId", defaultTemplateId);

src/main/java/edu/harvard/iq/dataverse/api/Admin.java

@@ -11,11 +11,14 @@
 import edu.harvard.iq.dataverse.DatasetVersionServiceBean;
 import edu.harvard.iq.dataverse.Dataverse;
 import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
+import edu.harvard.iq.dataverse.DataverseServiceBean;
 import edu.harvard.iq.dataverse.DataverseSession;
 import edu.harvard.iq.dataverse.DvObject;
 import edu.harvard.iq.dataverse.validation.EMailValidator;
 import edu.harvard.iq.dataverse.EjbDataverseEngine;
 import edu.harvard.iq.dataverse.GlobalId;
+import edu.harvard.iq.dataverse.Template;
+import edu.harvard.iq.dataverse.TemplateServiceBean;
 import edu.harvard.iq.dataverse.UserServiceBean;
 import edu.harvard.iq.dataverse.actionlogging.ActionLogRecord;
 import edu.harvard.iq.dataverse.api.dto.RoleDTO;
@@ -85,6 +88,7 @@
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import edu.harvard.iq.dataverse.engine.command.impl.DeactivateUserCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.DeleteRoleCommand;
+import edu.harvard.iq.dataverse.engine.command.impl.DeleteTemplateCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.RegisterDvObjectCommand;
 import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
@@ -101,6 +105,7 @@
 import static edu.harvard.iq.dataverse.util.json.JsonPrinter.json;
 import static edu.harvard.iq.dataverse.util.json.JsonPrinter.rolesToJson;
 import static edu.harvard.iq.dataverse.util.json.JsonPrinter.toJsonArray;
+import java.math.BigDecimal;
 
 
 import java.util.ArrayList;
@@ -140,6 +145,8 @@ public class Admin extends AbstractApiBean {
 	DataFileServiceBean fileService;
 	@EJB
 	DatasetServiceBean datasetService;
+        @EJB
+	DataverseServiceBean dataverseService;
 	@EJB
 	DatasetVersionServiceBean datasetversionService;
         @Inject
@@ -156,6 +163,8 @@ public class Admin extends AbstractApiBean {
         ExplicitGroupServiceBean explicitGroupService;
         @EJB
         BannerMessageServiceBean bannerMessageService;
+        @EJB
+        TemplateServiceBean templateService;
 
 	// Make the session available
 	@Inject
@@ -208,6 +217,75 @@ public Response deleteSetting(@PathParam("name") String name, @PathParam("lang")
 		settingsSvc.delete(name, lang);
 		return ok("Setting " + name + " - " + lang + " deleted.");
 	}
+
+    @Path("template/{id}")
+    @DELETE
+    public Response deleteTemplate(@PathParam("id") long id) {
+
+        AuthenticatedUser superuser = authSvc.getAdminUser();
+        if (superuser == null) {
+            return error(Response.Status.INTERNAL_SERVER_ERROR, "Cannot find superuser to execute DeleteTemplateCommand.");
+        }
+
+        Template doomed = templateService.find(id);
+        if (doomed == null) {
+            return error(Response.Status.NOT_FOUND, "Template with id " + id + " -  not found.");
+        }
+
+        Dataverse dv = doomed.getDataverse();
+        List <Dataverse> dataverseWDefaultTemplate = templateService.findDataversesByDefaultTemplateId(doomed.getId());
+
+        try {
+            commandEngine.submit(new DeleteTemplateCommand(createDataverseRequest(superuser), dv, doomed, dataverseWDefaultTemplate));
+        } catch (CommandException ex) {
+            Logger.getLogger(Admin.class.getName()).log(Level.SEVERE, null, ex);
+            return error(Response.Status.BAD_REQUEST, ex.getLocalizedMessage());
+        }
+
+        return ok("Template " + doomed.getName() + " deleted.");
+    }
+
+
+    @Path("templates")
+    @GET
+    public Response findAllTemplates() {
+        return findTemplates("");
+    }
+
+    @Path("templates/{alias}")
+    @GET
+    public Response findTemplates(@PathParam("alias") String alias) {
+        List<Template> templates;
+
+            if (alias.isEmpty()) {
+                templates = templateService.findAll();
+            } else {
+                try{
+                    Dataverse owner = findDataverseOrDie(alias);
+                    templates = templateService.findByOwnerId(owner.getId());
+                } catch (WrappedResponse r){
+                    return r.getResponse();
+                }
+            }
+
+            JsonArrayBuilder container = Json.createArrayBuilder();
+            for (Template t : templates) {
+                JsonObjectBuilder bld = Json.createObjectBuilder();
+                bld.add("templateId", t.getId());
+                bld.add("templateName", t.getName());
+                Dataverse loopowner = t.getDataverse();
+                if (loopowner != null) {
+                    bld.add("owner", loopowner.getDisplayName());
+                } else {
+                    bld.add("owner", "This an orphan template, it may be safely removed");
+                }
+                container.add(bld);
+            }
+
+            return ok(container);
+
+
+    }
 
 	@Path("authenticationProviderFactories")
 	@GET

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DeleteTemplateCommand.java

@@ -35,13 +35,17 @@ public DeleteTemplateCommand(DataverseRequest aRequest, Dataverse editedDv , Tem
 
     @Override
     public Dataverse execute(CommandContext ctxt) throws CommandException {
-        Dataverse merged = ctxt.em().merge(editedDv);
-        if (!dvWDefaultTemplate.isEmpty()){
-            for (Dataverse remove: dvWDefaultTemplate){
-                remove.setDefaultTemplate(null);
-                ctxt.em().merge(remove);
-            }                
+        Dataverse merged = null;
+        if (editedDv != null) {
+            merged = ctxt.em().merge(editedDv);
+            if (!dvWDefaultTemplate.isEmpty()) {
+                for (Dataverse remove : dvWDefaultTemplate) {
+                    remove.setDefaultTemplate(null);
+                    ctxt.em().merge(remove);
+                }
+            }
         }
+
         Template doomedAndMerged = ctxt.em().merge(doomed);
         ctxt.em().remove(doomedAndMerged);
         return merged;