dashboard and archive update

src/main/java/nl/fairbydesign/backend/ncbi/objects/esample/RUNSET.java

 package nl.fairbydesign.backend.ncbi.objects.esample;
 
-import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
+import java.util.ArrayList;
+
 
 public class RUNSET{
     @JsonProperty("RUN")
-    public RUN getRUN() {
+    public ArrayList<RUN> getRUN() {
 		 return this.rUN; }
-    public void setRUN(RUN rUN) {
+    public void setRUN(ArrayList<RUN> rUN) {
 		 this.rUN = rUN; }
-    RUN rUN;
-    }
-}
+    ArrayList<RUN> rUN = new ArrayList<>();
+    }
\ No newline at end of file

src/main/java/nl/fairbydesign/views/unlock/archive/Archive.java

@@ -28,6 +28,7 @@ import org.irods.jargon.core.pub.IRODSFileSystem;
 import org.irods.jargon.core.pub.domain.AvuData;
 import org.irods.jargon.core.pub.io.IRODSFile;
 import org.irods.jargon.core.pub.io.IRODSFileFactory;
+import org.irods.jargon.core.query.MetaDataAndDomainData;
 import org.jboss.logging.Logger;
 
 import java.util.ArrayList;
@@ -144,6 +145,7 @@ public class Archive extends Div {
             });
             dual.addClickListener(clicked -> {
                 // Set metadata to dual store (disk and archive)
+                Notification.show("Disk & Tape clicked");
                 sendTo(credentials, grid.getSelectedItems(), "to_dual");
                 // Force refresh of grid
                 searchButton.clickInClient();
@@ -164,12 +166,26 @@ public class Archive extends Div {
             IRODSAccessObjectFactory accessObjectFactory = IRODSFileSystem.instance().getIRODSAccessObjectFactory();
             for (File file : files) {
                 IRODSFile irodsFile = fileFactory.instanceIRODSFile(file.getPath());
-                AvuData avuData = new AvuData();
-                avuData.setAttribute("RESOURCE");
-                avuData.setValue(value);
-                avuData.setUnit("");
+                AvuData newAvuData = new AvuData();
+                newAvuData.setAttribute("RESOURCE");
+                newAvuData.setValue(value);
+                newAvuData.setUnit("");
                 DataObjectAO dataObjectAO = accessObjectFactory.getDataObjectAO(credentials.getIrodsAccount());
-                dataObjectAO.addAVUMetadata(file.getPath(), avuData);
+                boolean replaced = false;
+                for (MetaDataAndDomainData metaDataAndDomainData : dataObjectAO.findMetadataValuesForDataObject(irodsFile)) {
+                    AvuData avuDataIrodsFile = metaDataAndDomainData.asAvu();
+                    if (avuDataIrodsFile.getAttribute().contentEquals("RESOURCE")) {
+                        // Replace AVU object by this new one
+                        logger.info("Replacing AVU RESOURCE object");
+                        dataObjectAO.modifyAVUMetadata(irodsFile.getAbsolutePath(), avuDataIrodsFile, newAvuData);
+                        replaced = true;
+                        break;
+                    }
+                }
+                if (!replaced) {
+                    logger.info("Adding AVU RESOURCE object");
+                    dataObjectAO.addAVUMetadata(file.getPath(), newAvuData);
+                }
             }
         } catch (JargonException e) {
             e.printStackTrace();

src/main/java/nl/fairbydesign/views/unlock/dashboard/DashboardView.java

@@ -27,6 +27,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 
+import static nl.fairbydesign.backend.irods.Data.getDiskUsage;
 import static nl.fairbydesign.backend.irods.Data.getJobInformation;
 
 /**
@@ -51,7 +52,7 @@ public class DashboardView extends Div {
             // Drop down menu for projects?
             ArrayList<Process> processes = Data.getPIS(credentials.getIrodsAccount());
 
-            // Obtain disk usage overview
+            // Obtain disk usage overview for project and investigation in landingzone and projects
             ArrayList<DiskUsage> diskUsages = new ArrayList<>();
             HashSet<String> diskUsageAnalysed = new HashSet<>();
             for (Process process : processes) {
@@ -102,10 +103,33 @@ public class DashboardView extends Div {
             diskUsageGrid.removeAllColumns();
             diskUsageGrid.addColumn(DiskUsage::getProject).setHeader("Project");
             diskUsageGrid.addColumn(DiskUsage::getInvestigation).setHeader("Investigation");
-            diskUsageGrid.addColumn(DiskUsage::getSize).setHeader("Size (GB)");
+            diskUsageGrid.addColumn(DiskUsage::getTapeSize).setHeader("Tape size (GB)");
+            diskUsageGrid.addColumn(DiskUsage::getDiskSize).setHeader("Disk size (GB)");
 
             add(diskUsageGrid);
 
+            // Obtain overall disk usage
+            try {
+                Process process = new Process();
+                process.setProjectIdentifier("%");
+                process.setInvestigationIdentifier("%");
+                ArrayList<DiskUsage> irodsUsages = new ArrayList<>();
+                irodsUsages.add(getDiskUsage(credentials.getIrodsAccount(), process));
+
+                Grid<DiskUsage> iRODSUsageGrid = new Grid<>(DiskUsage.class);
+                iRODSUsageGrid.setItems(irodsUsages);
+                iRODSUsageGrid.removeAllColumns();
+                iRODSUsageGrid.addColumn(DiskUsage::getProject).setHeader("Project");
+                iRODSUsageGrid.addColumn(DiskUsage::getInvestigation).setHeader("Investigation");
+                iRODSUsageGrid.addColumn(DiskUsage::getTapeSize).setHeader("Tape size (GB)");
+                iRODSUsageGrid.addColumn(DiskUsage::getDiskSize).setHeader("Disk size (GB)");
+
+                add(iRODSUsageGrid);
+            } catch (GenQueryBuilderException | JargonException | JargonQueryException e) {
+                e.printStackTrace();
+            }
+
+
         } else {
             add(new Label("To use this you need to login first..."));
             Button button = new Button("Login", event -> UI.getCurrent().navigate("login"));