6230 changes for upcoming glassfish upgrade

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

@@ -6,6 +6,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
@@ -19,8 +20,8 @@
 @FacesConverter("controlledVocabularyValueConverter")
 public class ControlledVocabularyValueConverter implements Converter {
 
-    @EJB
-    DatasetFieldServiceBean datasetFieldService;
+    //@EJB
+    DatasetFieldServiceBean datasetFieldService = CDI.current().select(DatasetFieldServiceBean.class).get();
 
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {
         if (submittedValue == null || submittedValue.equals("")) {

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

@@ -2,6 +2,7 @@
 
 import java.util.logging.Logger;
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
@@ -13,8 +14,8 @@ public class DataFileConverter implements Converter {
 
     private static final Logger logger = Logger.getLogger(DataFileConverter.class.getCanonicalName());
 
-    @EJB
-    DataFileServiceBean dataFileService;
+    //@EJB
+    DataFileServiceBean dataFileService = CDI.current().select(DataFileServiceBean.class).get();
 
     @Override
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {

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

@@ -7,6 +7,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
 import javax.faces.convert.Converter;
@@ -15,8 +16,8 @@
 @FacesConverter("datasetConverter")
 public class DatasetConverter implements Converter {
 
-    @EJB
-    DatasetServiceBean datasetService;
+    //@EJB
+    DatasetServiceBean datasetService = CDI.current().select(DatasetServiceBean.class).get();
 
     @Override
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {

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

@@ -242,6 +242,8 @@ public enum DisplayMode {
     @Inject DataverseHeaderFragment dataverseHeaderFragment;
 
     private Dataset dataset = new Dataset();
+
+    private Long id = null;    
     private EditMode editMode;
     private boolean bulkFileDeleteInProgress = false;
 
@@ -1446,6 +1448,9 @@ public void setDataset(Dataset dataset) {
     public DatasetVersion getWorkingVersion() {
         return workingVersion;
     }
+
+    public Long getId() { return this.id; }
+    public void setId(Long id) { this.id = id; }    
 
     public EditMode getEditMode() {
         return editMode;
@@ -1799,9 +1804,9 @@ private String init(boolean initFull) {
                 this.workingVersion = retrieveDatasetVersionResponse.getDatasetVersion();
                 logger.fine("retrieved version: id: " + workingVersion.getId() + ", state: " + this.workingVersion.getVersionState());
 
-            } else if (dataset.getId() != null) {
+            } else if (this.getId() != null) {
                 // Set Working Version and Dataset by Datasaet Id and Version
-                dataset = datasetService.find(dataset.getId());
+                dataset = datasetService.find(this.getId());
                 if (dataset == null) {
                     logger.warning("No such dataset: "+dataset);
                     return permissionsWrapper.notFound();

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

@@ -6,6 +6,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
 import javax.faces.convert.Converter;
@@ -18,15 +19,15 @@
 @FacesConverter("datasetVersionConverter")
 public class DatasetVersionConverter implements Converter {
 
-    @EJB
-    DatasetVersionServiceBean datasetVersionService;
+    //@EJB
+    DatasetVersionServiceBean datasetVersionService = CDI.current().select(DatasetVersionServiceBean.class).get();
 
 
     @Override
     public Object getAsObject(FacesContext context, UIComponent component, String value) {
                 if (value == null || value.equals("")) {
             return "";
-        } else {
+        } else {                  
             return datasetVersionService.find(new Long(value));
         }
     }

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

@@ -7,6 +7,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
 import javax.faces.convert.Converter;
@@ -20,8 +21,8 @@
 public class DataverseConverter implements Converter {
 
 
-    @EJB
-    DataverseServiceBean dataverseService;
+    //@EJB
+    DataverseServiceBean dataverseService = CDI.current().select(DataverseServiceBean.class).get();
 
     @Override
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {

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

@@ -110,11 +110,17 @@ public enum LinkMode {
     @Inject PermissionsWrapper permissionsWrapper;
     @Inject DataverseHeaderFragment dataverseHeaderFragment; 
 
-    private Dataverse dataverse = new Dataverse();
+    private Dataverse dataverse = new Dataverse();  
+
+    /**
+     * View parameters
+     */
+    private Long id = null;
+    private String alias = null;
+    private Long ownerId = null;    
     private EditMode editMode;
     private LinkMode linkMode;
 
-    private Long ownerId;
     private DualListModel<DatasetFieldType> facets = new DualListModel<>(new ArrayList<>(), new ArrayList<>());
     private DualListModel<Dataverse> featuredDataverses = new DualListModel<>(new ArrayList<>(), new ArrayList<>());
     private List<Dataverse> dataversesForLinking;
@@ -266,6 +272,12 @@ public Dataverse getDataverse() {
     public void setDataverse(Dataverse dataverse) {
         this.dataverse = dataverse;
     }
+
+    public Long getId() { return this.id; }
+    public void setId(Long id) { this.id = id; }
+
+    public String getAlias() { return this.alias; }
+    public void setAlias(String alias) { this.alias = alias; }    
 
     public EditMode getEditMode() {
         return editMode;
@@ -298,11 +310,11 @@ public void updateOwnerDataverse() {
     public String init() {
         //System.out.println("_YE_OLDE_QUERY_COUNTER_");  // for debug purposes
 
-        if (dataverse.getAlias() != null || dataverse.getId() != null || ownerId == null) {// view mode for a dataverse
-            if (dataverse.getAlias() != null) {
-                dataverse = dataverseService.findByAlias(dataverse.getAlias());
-            } else if (dataverse.getId() != null) {
-                dataverse = dataverseService.find(dataverse.getId());
+        if (this.getAlias() != null || this.getId() != null || this.getOwnerId() == null) {// view mode for a dataverse
+            if (this.getAlias() != null) {
+                dataverse = dataverseService.findByAlias(this.getAlias());
+            } else if (this.getId() != null) {
+                dataverse = dataverseService.find(this.getId());
             } else {
                 try {
                     dataverse = dataverseService.findRootDataverse();
@@ -323,7 +335,7 @@ public String init() {
             ownerId = dataverse.getOwner() != null ? dataverse.getOwner().getId() : null;
         } else { // ownerId != null; create mode for a new child dataverse
             editMode = EditMode.CREATE;
-            dataverse.setOwner(dataverseService.find(ownerId));
+            dataverse.setOwner(dataverseService.find( this.getOwnerId()));
             if (dataverse.getOwner() == null) {
                 return  permissionsWrapper.notFound();
             } else if (!permissionService.on(dataverse.getOwner()).has(Permission.AddDataverse)) {

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

@@ -6,6 +6,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
@@ -19,8 +20,8 @@
 @FacesConverter("facetConverter")
 public class FacetConverter implements Converter {
 
-    @EJB
-    DatasetFieldServiceBean datasetFieldService;
+    //@EJB
+    DatasetFieldServiceBean datasetFieldService = CDI.current().select(DatasetFieldServiceBean.class).get();
 
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {
         return datasetFieldService.find(new Long(submittedValue));

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

@@ -6,6 +6,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
@@ -19,8 +20,8 @@
 @FacesConverter("metadataBlockConverter")
 public class MetadataBlockConverter implements Converter {
 
-    @EJB
-    DataverseServiceBean dataverseService;
+    //@EJB
+    DataverseServiceBean dataverseService = CDI.current().select(DataverseServiceBean.class).get();
 
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {
         MetadataBlock mdb = dataverseService.findMDB(new Long(submittedValue));

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

@@ -7,9 +7,8 @@
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.authorization.RoleAssignee;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
@@ -23,8 +22,8 @@
 @FacesConverter("roleAssigneeConverter")
 public class RoleAssigneeConverter implements Converter {
 
-    @EJB
-    RoleAssigneeServiceBean roleAssigneeService;
+    //@EJB
+    RoleAssigneeServiceBean roleAssigneeService = CDI.current().select(RoleAssigneeServiceBean.class).get();
 
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {
         RoleAssignee mdb = roleAssigneeService.getRoleAssignee(submittedValue);

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

@@ -7,6 +7,7 @@
 package edu.harvard.iq.dataverse;
 
 import javax.ejb.EJB;
+import javax.enterprise.inject.spi.CDI;
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
 import javax.faces.convert.Converter;
@@ -19,8 +20,8 @@
 @FacesConverter("templateConverter")
 public class TemplateConverter implements Converter {
 
-    @EJB
-    TemplateServiceBean templateService;
+    //@EJB
+    TemplateServiceBean templateService = CDI.current().select(TemplateServiceBean.class).get();
 
     @Override
     public Object getAsObject(FacesContext facesContext, UIComponent component, String submittedValue) {

src/main/java/edu/harvard/iq/dataverse/provenance/ProvEntityFileDataConverter.java

@@ -1,5 +1,6 @@
 package edu.harvard.iq.dataverse.provenance;
 
+import javax.enterprise.inject.spi.CDI;
 import javax.faces.component.UIComponent;
 import javax.faces.context.FacesContext;
 import javax.faces.convert.Converter;
@@ -14,8 +15,8 @@
 @FacesConverter("provEntityFileDataConverter")
 public class ProvEntityFileDataConverter implements Converter{
 
-    @Inject
-    ProvPopupFragmentBean provBean;
+    //@Inject
+    ProvPopupFragmentBean provBean = CDI.current().select(ProvPopupFragmentBean.class).get();
 
     @Override
     public Object getAsObject(FacesContext context, UIComponent component, String value) {

src/main/webapp/dataset.xhtml

@@ -9,8 +9,7 @@
       xmlns:jsf="http://xmlns.jcp.org/jsf"
       xmlns:pt="http://java.sun.com/jsf/passthrough"
       xmlns:cc="http://java.sun.com/jsf/composite"
-      xmlns:o="http://omnifaces.org/ui"
-      xmlns:iqbs="http://xmlns.jcp.org/jsf/composite/iqbs">
+      xmlns:o="http://omnifaces.org/ui">
     <h:head>
     </h:head>
     <h:body>
@@ -58,8 +57,8 @@
             <ui:define name="body">
                 <o:importFunctions type="edu.harvard.iq.dataverse.util.MarkupChecker" />
                 <f:metadata>
-                    <f:viewParam name="id" value="#{DatasetPage.dataset.id}"/>
-                    <f:viewParam name="ownerId" value="#{DatasetPage.ownerId}"/>
+                    <f:viewParam name="id" value="#{DatasetPage.id}"/>
+                    <o:viewParam name="ownerId" value="#{DatasetPage.ownerId}"/>
                     <f:viewParam name="version" value="#{DatasetPage.version}"/>
                     <f:viewParam name="versionId" value="#{DatasetPage.versionId}"/>
                     <f:viewParam name="persistentId" value="#{DatasetPage.persistentId}"/>
@@ -631,6 +630,7 @@
                             <p:commandButton id="refreshButton" process="@this" widgetVar="refreshButton" update=":datasetForm:topDatasetBlockFragment,:datasetForm:tabView:filesTable" style="display:none"/>
                             <script>
                                 //<![CDATA[
+                                // javascript for refreshing page when locks
                                 $(this).ready(function () {
                                     refreshIfStillLocked();
                                 });

src/main/webapp/dataverse.xhtml

@@ -19,10 +19,10 @@
             </ui:define>
             <ui:define name="body">
                 <f:metadata>
-                    <f:viewParam name="id" value="#{DataversePage.dataverse.id}"/>
-                    <f:viewParam name="alias" value="#{DataversePage.dataverse.alias}"/>
+                    <f:viewParam name="id" value="#{DataversePage.id}"/>
+                    <f:viewParam name="alias" value="#{DataversePage.alias}"/>
                     <f:viewParam name="ownerId" value="#{DataversePage.ownerId}"/>
-                    <f:viewParam name="editMode" value="#{DataversePage.editMode}"/>
+                    <o:viewParam name="editMode" value="#{DataversePage.editMode}"/>
                     <f:viewAction action="#{dataverseSession.updateLocaleInViewRoot}"/>
                     <f:viewAction action="#{DataversePage.init}"/>
                     <f:viewAction action="#{dataverseHeaderFragment.initBreadcrumbs(DataversePage.dataverse)}"/>
@@ -370,7 +370,7 @@
                         </p:panel>
                         <!-- Save / Cancel Button Panel -->
                         <div class="button-block">
-                            <p:commandButton id="save" styleClass="btn btn-default" value="#{DataversePage.dataverse.id == null ? bundle.createDataverse : bundle.saveChanges}" action="#{DataversePage.save}" update="@all">
+                            <p:commandButton id="save" styleClass="btn btn-default" value="#{DataversePage.dataverse.id == null ? bundle.createDataverse : bundle.saveChanges}" action="#{DataversePage.save}" update="@form :messagePanel">
                                 <f:ajax onerror="window.scrollTo(0, 0)" />
                             </p:commandButton>
                             <p:commandButton id="cancel" styleClass="btn btn-link" value="#{bundle.cancel}" action="#{DataversePage.cancel}" rendered="#{DataversePage.dataverse.id != null}"/>

src/main/webapp/dataverseuser.xhtml

@@ -29,7 +29,7 @@
                 <f:loadBundle basename="propertyFiles.Bundle" var="bundle"/>
                 <f:metadata>
                     <f:event type="preRenderView" listener="#{facesContext.externalContext.response.setHeader('Cache-Control', 'no-cache, no-store')}"/>
-                    <f:viewParam name="editMode" value="#{DataverseUserPage.editMode}"/>
+                    <o:viewParam name="editMode" value="#{DataverseUserPage.editMode}"/>
                     <f:viewParam name="redirectPage" value="#{DataverseUserPage.redirectPage}"/>
                     <f:viewParam name="selectTab" value="#{DataverseUserPage.selectTab}"/>
                     <f:viewAction action="#{dataverseSession.updateLocaleInViewRoot}"/>