Removed the dvobjectConatainerTable #1545, added creators to DvObjects (

#983)
IQSS · Mar 2, 2015 · 18e84f1 · 18e84f1
1 parent 13a7fea
commit 18e84f1
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Showing 14 changed files with 159 additions and 174 deletions.
diff --git a/src/main/java/Bundle.properties b/src/main/java/Bundle.properties
@@ -232,6 +232,7 @@ dataverse.delete.success=Your dataverse has been deleted.
 dataverse.delete.failure=This dataverse was not able to be deleted.
 dataverse.create.success=You have successfully created your dataverse! To learn more about what you can do with your dataverse, check out the <a href='http://guides.dataverse.org/en/latest/user/dataverse-management.html'>User Guide</a>.
 dataverse.create.failure=This dataverse was not able to be created.
+dataverse.create.authenticatedUsersOnly=Only authenticated users can create dataverses.
 dataverse.update.success=You have successfully updated your dataverse!
 dataverse.update.failure=This dataverse was not able to be updated.
 
@@ -596,6 +597,7 @@ dataset.cite.whyCite.tip=If you use these data, please add this citation to your
 dataset.cite.downloadBtn=Download Citation
 dataset.cite.downloadBtn.xml=EndNote XML
 dataset.cite.downloadBtn.ris=RIS Format
+dataset.create.authenticatedUsersOnly=Only authenticated users can create datasets.
 dataset.deaccession.reason=Deaccession Reason:
 dataset.beAccessedAt=The dataset can now be accessed at:
 dataset.keywordDisplay.title=Keyword

diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java
@@ -10,9 +10,11 @@
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
 import edu.harvard.iq.dataverse.authorization.users.GuestUser;
 import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
+import java.util.Collections;
 import java.util.Date;
 import java.util.List;
 import java.util.UUID;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
@@ -135,16 +137,20 @@ public List<DataFile> findByDatasetId(Long studyId) {
            Sure, we don't have *studies* any more, in 4.0; it's a tribute 
            to the past. -- L.A.
         */
-        Query query = em.createQuery("select object(o) from DataFile as o where o.dataset.id =:studyId order by o.id");
+        Query query = em.createQuery("select o from DataFile o where o.owner.id = :studyId order by o.id");
         query.setParameter("studyId", studyId);
         return query.getResultList();
     }  
 
     public List<DataFile> findIngestsInProgress() {
-        Query query = em.createQuery("select object(o) from DataFile as o where o.ingestStatus =:scheduledStatusCode or o.ingestStatus =:progressStatusCode order by o.id");
-        query.setParameter("scheduledStatusCode", DataFile.INGEST_STATUS_SCHEDULED);
-        query.setParameter("progressStatusCode", DataFile.INGEST_STATUS_INPROGRESS);
-        return query.getResultList();
+        if ( em.isOpen() ) {
+            Query query = em.createQuery("select object(o) from DataFile as o where o.ingestStatus =:scheduledStatusCode or o.ingestStatus =:progressStatusCode order by o.id");
+            query.setParameter("scheduledStatusCode", DataFile.INGEST_STATUS_SCHEDULED);
+            query.setParameter("progressStatusCode", DataFile.INGEST_STATUS_INPROGRESS);
+            return query.getResultList();
+        } else {
+            return Collections.emptyList();
+        }
     }
 
     public DataTable findDataTableByFileId(Long fileId) {
@@ -181,25 +187,24 @@ public void generateStorageIdentifier(DataFile dataFile) {
     }
 
     public String generateStorageIdentifier() {
-        String storageIdentifier = null; 
 
         UUID uid = UUID.randomUUID();
 
-        logger.fine("UUID value: "+uid.toString());
+        logger.log(Level.FINE, "UUID value: {0}", uid.toString());
 
         // last 6 bytes, of the random UUID, in hex: 
 
         String hexRandom = uid.toString().substring(24);
 
-        logger.fine("UUID (last 6 bytes, 12 hex digits): "+hexRandom);
+        logger.log(Level.FINE, "UUID (last 6 bytes, 12 hex digits): {0}", hexRandom);
 
         String hexTimestamp = Long.toHexString(new Date().getTime());
 
-        logger.fine("(not UUID) timestamp in hex: "+hexTimestamp);
+        logger.log(Level.FINE, "(not UUID) timestamp in hex: {0}", hexTimestamp);
 
-        storageIdentifier = hexTimestamp + "-" + hexRandom;
+        String storageIdentifier = hexTimestamp + "-" + hexRandom;
 
-        logger.fine("timestamp/UUID hybrid: "+storageIdentifier);
+        logger.log(Level.FINE, "timestamp/UUID hybrid: {0}", storageIdentifier);
         return storageIdentifier; 
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -1,13 +1,7 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
 import edu.harvard.iq.dataverse.authorization.Permission;
-import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUser;
 import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
 import edu.harvard.iq.dataverse.authorization.users.ApiToken;
 import edu.harvard.iq.dataverse.authorization.users.User;
@@ -1333,7 +1327,7 @@ public String save() {
                      */
                     try {
                         Long idToRemove = fmd.getId(); ///dfn.getId();
-                        logger.info("deleting file, filemetadata id " + idToRemove);
+                        logger.log(Level.INFO, "deleting file, filemetadata id {0}", idToRemove);
 
                         // finally, check if this file is being used as the default thumbnail
                         // for its dataset: 
@@ -1390,8 +1384,13 @@ public String save() {
         try {
             if (editMode == EditMode.CREATE) {
                 workingVersion.setLicense(DatasetVersion.License.CC0);
-                if(selectedTemplate != null){
-                   cmd = new CreateDatasetCommand(dataset, session.getUser(), false, null, selectedTemplate); 
+                if ( selectedTemplate != null ) {
+                    if ( session.getUser().isAuthenticated() ) {
+                        cmd = new CreateDatasetCommand(dataset, (AuthenticatedUser) session.getUser(), false, null, selectedTemplate); 
+                    } else {
+                        JH.addMessage(FacesMessage.SEVERITY_FATAL, JH.localize("dataset.create.authenticatedUsersOnly"));
+                        return null;
+                    }
                 } else {
                    cmd = new CreateDatasetCommand(dataset, session.getUser());
                 }
@@ -1407,15 +1406,15 @@ public String save() {
             }
         } catch (EJBException ex) {
             StringBuilder error = new StringBuilder();
-            error.append(ex + " ");
-            error.append(ex.getMessage() + " ");
+            error.append(ex).append(" ");
+            error.append(ex.getMessage()).append(" ");
             Throwable cause = ex;
-            while (cause.getCause() != null) {
+            while (cause.getCause()!= null) {
                 cause = cause.getCause();
-                error.append(cause + " ");
-                error.append(cause.getMessage() + " ");
+                error.append(cause).append(" ");
+                error.append(cause.getMessage()).append(" ");
             }
-            logger.fine("Couldn't save dataset: " + error.toString());
+            logger.log(Level.FINE, "Couldn''t save dataset: {0}", error.toString());
             populateDatasetUpdateFailureMessage();
             return null;
         } catch (CommandException ex) {

diff --git a/src/main/java/edu/harvard/iq/dataverse/DataversePage.java b/src/main/java/edu/harvard/iq/dataverse/DataversePage.java
@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.UserNotification.Type;
@@ -514,9 +509,14 @@ public String save(String message) {
         //TODO change to Create - for now the page is expecting INFO instead.
         Boolean create;
         if (dataverse.getId() == null) {
-            dataverse.setOwner(ownerId != null ? dataverseService.find(ownerId) : null);
-            create = Boolean.TRUE;
-            cmd = new CreateDataverseCommand(dataverse, session.getUser(), facets.getTarget(), listDFTIL);
+            if ( session.getUser().isAuthenticated() ) {
+                dataverse.setOwner(ownerId != null ? dataverseService.find(ownerId) : null);
+                create = Boolean.TRUE;
+                cmd = new CreateDataverseCommand(dataverse, (AuthenticatedUser) session.getUser(), facets.getTarget(), listDFTIL);
+            } else {
+                JH.addMessage(FacesMessage.SEVERITY_FATAL, JH.localize("dataverse.create.authenticatedUsersOnly"));
+                return null;
+            }
         } else {
             create=Boolean.FALSE;
             cmd = new UpdateDataverseCommand(dataverse, facets.getTarget(), featuredDataverses.getTarget(), session.getUser(), listDFTIL);

diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObject.java b/src/main/java/edu/harvard/iq/dataverse/DvObject.java
@@ -50,7 +50,7 @@ public String visit(DataFile df) {
     private Long id;
 
     @ManyToOne(cascade = CascadeType.MERGE)
-    private DvObjectContainer owner;
+    private DvObject owner;
 
     private Timestamp publicationDate;
 
@@ -85,6 +85,7 @@ public Timestamp getModificationTime() {
     /**
      * modificationTime is used for comparison with indexTime so we know if the
      * Solr index is stale.
+     * @param modificationTime
      */
     public void setModificationTime(Timestamp modificationTime) {
         this.modificationTime = modificationTime;
@@ -97,6 +98,7 @@ public Timestamp getIndexTime() {
     /**
      * indexTime is used for comparison with modificationTime so we know if the
      * Solr index is stale.
+     * @param indexTime
      */
     public void setIndexTime(Timestamp indexTime) {
         this.indexTime = indexTime;
@@ -123,7 +125,7 @@ protected void setOwner(DvObjectContainer newOwner) {
     }
 
     public DvObjectContainer getOwner() {
-        return owner;
+        return (DvObjectContainer)owner;
     }
 
     public Long getId() {

diff --git a/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java b/src/main/java/edu/harvard/iq/dataverse/DvObjectContainer.java
@@ -1,13 +1,13 @@
 package edu.harvard.iq.dataverse;
 
-import javax.persistence.Entity;
+import javax.persistence.MappedSuperclass;
 
 /**
  * A {@link DvObject} that can contain other {@link DvObject}s.
  * 
  * @author michael
  */
-@Entity
+@MappedSuperclass
 public abstract class DvObjectContainer extends DvObject {
 
     public void setOwner(Dataverse owner) {

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java b/src/main/java/edu/harvard/iq/dataverse/api/BatchImport.java
@@ -8,13 +8,12 @@
 
 import edu.harvard.iq.dataverse.api.imports.ImportException;
 import edu.harvard.iq.dataverse.api.imports.ImportUtil.ImportType;
+import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
 import edu.harvard.iq.dataverse.authorization.users.User;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
-import edu.harvard.iq.dataverse.util.ImportLogger;
 import java.io.IOException;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
-import javax.inject.Inject;
 import javax.json.JsonObjectBuilder;
 import javax.ws.rs.GET;
 import javax.ws.rs.POST;
@@ -107,7 +106,7 @@ public Response getImport(@QueryParam("path") String fileDir, @QueryParam("ident
 
     private Response startBatchJob( String fileDir, String parentIdtf, String apiKey, ImportType importType) {
 
-        User u = findUserByApiToken(apiKey);
+        AuthenticatedUser u = findUserByApiToken(apiKey);
         if (u == null) {
             return badApiKey(apiKey);
         }

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/api/BatchServiceBean.java
@@ -1,18 +1,12 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package edu.harvard.iq.dataverse.api;
 
 import edu.harvard.iq.dataverse.Dataverse;
 import edu.harvard.iq.dataverse.DataverseServiceBean;
 import edu.harvard.iq.dataverse.api.imports.ImportException;
 import edu.harvard.iq.dataverse.api.imports.ImportUtil;
-import edu.harvard.iq.dataverse.authorization.users.User;
+import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
 import edu.harvard.iq.dataverse.util.ImportLogger;
 import java.io.File;
-import java.io.IOException;
 import javax.ejb.Asynchronous;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
@@ -35,7 +29,7 @@ public class BatchServiceBean {
     ImportLogger importLogger;
 
     @Asynchronous
-    public void processFilePath(String fileDir, String parentIdtf, User u, Dataverse owner, ImportUtil.ImportType importType) throws ImportException {
+    public void processFilePath(String fileDir, String parentIdtf, AuthenticatedUser u, Dataverse owner, ImportUtil.ImportType importType) throws ImportException {
         importLogger.getLogger().info("BEGIN IMPORT");
         JsonArrayBuilder status = Json.createArrayBuilder();
 
@@ -59,7 +53,7 @@ public void processFilePath(String fileDir, String parentIdtf, User u, Dataverse
 
     }
 
-    public JsonArrayBuilder handleDirectory(User u, File dir, ImportUtil.ImportType importType) throws ImportException{
+    public JsonArrayBuilder handleDirectory(AuthenticatedUser u, File dir, ImportUtil.ImportType importType) throws ImportException{
         JsonArrayBuilder status = Json.createArrayBuilder();
         Dataverse owner = dataverseService.findByAlias(dir.getName());
         if (owner == null) {

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java
@@ -118,7 +118,7 @@ public Response addDataverse( String body, @PathParam("identifier") String paren
                 dc.setDataverse(d);
             }
 
-            User u = findUserOrDie( apiKey );
+            AuthenticatedUser u = findUserOrDie( apiKey );
             d = execCommand( new CreateDataverseCommand(d, u, null, null), "Creating Dataverse" );
 			return createdResponse( "/dvs/"+d.getAlias(), json(d) );
         } catch ( WrappedResponse ww ) {