From 2fc5993572446fdf7eb700bd625f6da03c205d67 Mon Sep 17 00:00:00 2001
From: schauderd <schauderd@janelia.hhmi.org>
Date: Tue, 4 Mar 2025 09:24:02 -0500
Subject: [PATCH 1/2] added Db Cleanup option to remove large TmWorkspaces

---
 .../admin/AdministrationTopComponent.java     |  40 +++-
 .../admin/DatabaseCleanupPanel.java           | 225 ++++++++++++++++++
 .../workstation/admin/images/clean.png        | Bin 0 -> 4674 bytes
 .../janelia/workstation/admin/images/logs.png | Bin 5015 -> 5937 bytes
 .../access/TiledMicroscopeDomainMgr.java      |  11 +
 .../access/TiledMicroscopeRestClient.java     |  31 +++
 pom.xml                                       |   2 +-
 7 files changed, 300 insertions(+), 9 deletions(-)
 create mode 100644 modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java
 create mode 100644 modules/AdministrationGUI/src/main/resources/org/janelia/workstation/admin/images/clean.png

diff --git a/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/AdministrationTopComponent.java b/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/AdministrationTopComponent.java
index 74485408a..782aee2a8 100644
--- a/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/AdministrationTopComponent.java
+++ b/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/AdministrationTopComponent.java
@@ -77,9 +77,11 @@ private void setupGUI() {
         setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
 
         this.topMenu = new JPanel();
-        BoxLayout layout = new BoxLayout(topMenu, BoxLayout.X_AXIS);
-        topMenu.setLayout(layout);
+        topMenu.setLayout(new BoxLayout(topMenu, BoxLayout.Y_AXIS)); // Main panel with vertical layout
 
+        // First row with "Users" and "Groups"
+        JPanel row1 = new JPanel();
+        row1.setLayout(new BoxLayout(row1, BoxLayout.X_AXIS));
         // top level buttons
         JButton listUsersButton = new JButton(UIUtils.getClasspathImage(this.getClass(), "/org/janelia/workstation/admin/images/user.png"));
         listUsersButton.setText("Users");
@@ -87,9 +89,9 @@ private void setupGUI() {
         listUsersButton.setVerticalTextPosition(SwingConstants.BOTTOM);
         listUsersButton.setHorizontalTextPosition(SwingConstants.CENTER);
         listUsersButton.addActionListener(event -> viewUserList());
-        topMenu.add(listUsersButton);
+        row1.add(listUsersButton);
 
-        topMenu.add(Box.createHorizontalStrut(20));
+        row1.add(Box.createHorizontalStrut(20)); // Add space between buttons
 
         JButton listGroupsButton = new JButton(UIUtils.getClasspathImage(this.getClass(), "/org/janelia/workstation/admin/images/group.png"));
         listGroupsButton.setText("Groups");
@@ -97,17 +99,30 @@ private void setupGUI() {
         listGroupsButton.setToolTipText("Show all groups");
         listGroupsButton.setVerticalTextPosition(SwingConstants.BOTTOM);
         listGroupsButton.setHorizontalTextPosition(SwingConstants.CENTER);
-        topMenu.add(listGroupsButton);
-
-        topMenu.add(Box.createHorizontalStrut(20));
+        listGroupsButton.addActionListener(event -> viewGroupList());
+        row1.add(listGroupsButton);
 
+        row1.add(Box.createHorizontalStrut(20));
         JButton getLogsButton = new JButton(UIUtils.getClasspathImage(this.getClass(), "/org/janelia/workstation/admin/images/logs.png"));
         getLogsButton.setText("Logs");
         getLogsButton.setToolTipText("Retrieve Logs");
         getLogsButton.addActionListener(event -> getLogs());
         getLogsButton.setVerticalTextPosition(SwingConstants.BOTTOM);
         getLogsButton.setHorizontalTextPosition(SwingConstants.CENTER);
-        topMenu.add(getLogsButton);
+        row1.add(getLogsButton);
+
+        row1.add(Box.createHorizontalStrut(20));
+
+        JButton workspaceCleanupButton = new JButton(UIUtils.getClasspathImage(this.getClass(), "/org/janelia/workstation/admin/images/clean.png"));
+        workspaceCleanupButton.setText("Cleanup Db");
+        workspaceCleanupButton.setToolTipText("Manage and delete large workspaces");
+        workspaceCleanupButton.setVerticalTextPosition(SwingConstants.BOTTOM);
+        workspaceCleanupButton.setHorizontalTextPosition(SwingConstants.CENTER);
+        workspaceCleanupButton.addActionListener(event -> databaseCleanup());
+        row1.add(workspaceCleanupButton);
+
+        // Add both rows to the main menu
+        topMenu.add(row1);
 
         add(topMenu);
         add(Box.createVerticalGlue());
@@ -127,6 +142,15 @@ public void objectsInvalidated(DomainObjectInvalidationEvent event) {
         }
     }
 
+    void databaseCleanup() {
+        DatabaseCleanupPanel panel = new DatabaseCleanupPanel(this);
+        removeAll();
+        add(panel);
+        revalidate();
+        repaint();
+        this.currentView = panel;
+    }
+
     void viewUserList() {
         UserManagementPanel panel = new UserManagementPanel(this);
         removeAll();
diff --git a/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java b/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java
new file mode 100644
index 000000000..5fd3922f7
--- /dev/null
+++ b/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java
@@ -0,0 +1,225 @@
+package org.janelia.workstation.admin;
+
+import org.janelia.model.domain.tiledMicroscope.TmWorkspace;
+import org.janelia.model.domain.tiledMicroscope.TmWorkspaceInfo;
+import org.janelia.workstation.common.gui.support.DesktopApi;
+import org.janelia.workstation.controller.access.TiledMicroscopeDomainMgr;
+import org.janelia.workstation.core.util.Refreshable;
+import org.janelia.workstation.core.workers.BackgroundWorker;
+import org.janelia.workstation.core.workers.SimpleWorker;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.swing.*;
+import javax.swing.table.AbstractTableModel;
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.Callable;
+
+public class DatabaseCleanupPanel extends JPanel implements Refreshable {
+    private static final Logger log = LoggerFactory.getLogger(DatabaseCleanupPanel.class);
+    private final AdministrationTopComponent parent;
+    private JTable workspaceTable;
+    private WorkspaceTableModel tableModel;
+
+    public DatabaseCleanupPanel(AdministrationTopComponent parent) {
+        this.parent = parent;
+        refresh();
+    }
+
+    private void setupUI() {
+        setLayout(new BorderLayout());
+        removeAll();
+
+        JPanel titlePanel = new TitlePanel("Manage Workspaces", "Return To Top Menu",
+                event -> refresh(),
+                event -> returnHome());
+        add(titlePanel, BorderLayout.NORTH);
+
+        tableModel = new WorkspaceTableModel();
+        workspaceTable = new JTable(tableModel);
+        JScrollPane scrollPane = new JScrollPane(workspaceTable);
+        add(scrollPane, BorderLayout.CENTER);
+
+        JButton refreshButton = new JButton("Load Largest Workspaces");
+        refreshButton.addActionListener(e -> loadLargestWorkspaces());
+
+        JButton deleteButton = new JButton("Delete Selected Workspaces");
+        deleteButton.addActionListener(e -> deleteSelectedWorkspaces());
+
+        JPanel buttonPanel = new JPanel();
+        buttonPanel.add(refreshButton);
+        buttonPanel.add(deleteButton);
+        add(buttonPanel, BorderLayout.SOUTH);
+
+        revalidate();
+    }
+
+    private void loadLargestWorkspaces() {
+        SimpleWorker worker = new SimpleWorker() {
+            private List<TmWorkspaceInfo> workspaceResults;
+
+            @Override
+            protected void doStuff() {
+                SwingUtilities.invokeLater(() -> tableModel.clear());
+
+                TiledMicroscopeDomainMgr domainMgr = TiledMicroscopeDomainMgr.getDomainMgr();
+                workspaceResults = domainMgr.getLargestWorkspaces();
+            }
+
+            @Override
+            protected void hadSuccess() {
+                tableModel.setWorkspaces(workspaceResults);
+            }
+
+            @Override
+            protected void hadError(Throwable error) {
+                log.error("Error loading workspaces", error);
+                JOptionPane.showMessageDialog(DatabaseCleanupPanel.this,
+                        "Failed to load workspaces: " + error.getMessage(), "Error",
+                        JOptionPane.ERROR_MESSAGE);
+            }
+        };
+        worker.execute();
+    }
+
+    private void deleteSelectedWorkspaces() {
+        List<Long> selectedWorkspaces = tableModel.getSelectedWorkspaces();
+        if (selectedWorkspaces.isEmpty()) {
+            JOptionPane.showMessageDialog(this, "Please select at least one workspace to delete.", "No Selection", JOptionPane.WARNING_MESSAGE);
+            return;
+        }
+
+        int confirmation = JOptionPane.showConfirmDialog(this,
+                "Are you sure you want to delete the selected workspaces?",
+                "Confirm Deletion", JOptionPane.YES_NO_OPTION);
+
+        if (confirmation == JOptionPane.YES_OPTION) {
+
+            BackgroundWorker deleter = new BackgroundWorker() {
+                @Override
+                public String getName() {
+                    return "Deleting TmWorkspaces";
+                }
+
+                @Override
+                protected void doStuff() {
+                    TiledMicroscopeDomainMgr domainMgr = TiledMicroscopeDomainMgr.getDomainMgr();
+                    domainMgr.removeWorkspaces(selectedWorkspaces);
+                }
+
+                @Override
+                protected void hadSuccess() {
+                    loadLargestWorkspaces();
+                    JOptionPane.showMessageDialog(DatabaseCleanupPanel.this,
+                            "Selected workspaces deleted successfully.", "Success", JOptionPane.INFORMATION_MESSAGE);
+                }
+
+                @Override
+                protected void hadError(Throwable error) {
+                    log.error("Error deleting workspaces", error);
+                    JOptionPane.showMessageDialog(DatabaseCleanupPanel.this,
+                            "Failed to delete workspaces: " + error.getMessage(), "Error",
+                            JOptionPane.ERROR_MESSAGE);
+                }
+            };
+            deleter.executeWithEvents();
+        }
+    }
+
+    @Override
+    public void refresh() {
+        setupUI();
+    }
+
+    private void returnHome() {
+        parent.viewTopMenu();
+    }
+}
+
+class WorkspaceTableModel extends AbstractTableModel {
+    private final String[] columnNames = {"Select", "Name", "Owner", "Date Created", "Size"};
+    private List<TmWorkspaceInfo> workspaceResults = new ArrayList<>();
+    private final List<Boolean> selected = new ArrayList<>();
+
+    public void setWorkspaces(List<TmWorkspaceInfo> workspaceResults) {
+        this.workspaceResults = workspaceResults;
+        selected.clear();
+        for (int i = 0; i < workspaceResults.size(); i++) {
+            selected.add(false);  // Initialize selection state
+        }
+        fireTableDataChanged();
+    }
+
+    @Override
+    public int getRowCount() {
+        return workspaceResults.size();
+    }
+
+    @Override
+    public int getColumnCount() {
+        return columnNames.length;
+    }
+
+    @Override
+    public Object getValueAt(int rowIndex, int columnIndex) {
+        TmWorkspaceInfo workspaceInfo = workspaceResults.get(rowIndex);
+        switch (columnIndex) {
+            case 0:
+                return selected.get(rowIndex);  // Boolean checkbox
+            case 1:
+                return workspaceInfo.getWorkspaceName();
+            case 2:
+                return workspaceInfo.getOwnerKey();
+            case 3:
+                return workspaceInfo.getDateCreated();
+            case 4:
+                return workspaceInfo.getTotalSize();
+            default:
+                return null;
+        }
+    }
+
+    @Override
+    public boolean isCellEditable(int rowIndex, int columnIndex) {
+        return columnIndex == 0;  // Allow only checkboxes to be editable
+    }
+
+    @Override
+    public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
+        if (columnIndex == 0 && aValue instanceof Boolean) {
+            selected.set(rowIndex, (Boolean) aValue);
+            fireTableCellUpdated(rowIndex, columnIndex);  // Notify JTable of the change
+        }
+    }
+
+    public void clear() {
+        workspaceResults.clear();
+        selected.clear();
+        fireTableDataChanged(); // Notify the table UI that the data has changed
+    }
+
+    @Override
+    public Class<?> getColumnClass(int columnIndex) {
+        return columnIndex == 0 ? Boolean.class : String.class;
+    }
+
+    public List<Long> getSelectedWorkspaces() {
+        List<Long> selectedWorkspaces = new ArrayList<>();
+        for (int i = 0; i < workspaceResults.size(); i++) {
+            if (selected.get(i)) {
+                selectedWorkspaces.add(workspaceResults.get(i).getWorkspaceId());
+            }
+        }
+        return selectedWorkspaces;
+    }
+
+    @Override
+    public String getColumnName(int column) {
+        return columnNames[column];
+    }
+}
+
diff --git a/modules/AdministrationGUI/src/main/resources/org/janelia/workstation/admin/images/clean.png b/modules/AdministrationGUI/src/main/resources/org/janelia/workstation/admin/images/clean.png
new file mode 100644
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diff --git a/modules/AdministrationGUI/src/main/resources/org/janelia/workstation/admin/images/logs.png b/modules/AdministrationGUI/src/main/resources/org/janelia/workstation/admin/images/logs.png
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delta 1261
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z1N7Wme0!O(KSUng2jp&aqi2e@!Y%-V0MaKz>-s?}aVmrSd<g{2>2KvEayT3gheHT|
Xi17%L9NDVj00000NkvXXu0mjfb?+bU

diff --git a/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeDomainMgr.java b/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeDomainMgr.java
index 2e037dabb..a1cf84b81 100644
--- a/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeDomainMgr.java
+++ b/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeDomainMgr.java
@@ -15,6 +15,7 @@
 import org.janelia.workstation.core.events.Events;
 import org.janelia.workstation.core.events.lifecycle.ConsolePropsLoaded;
 import org.janelia.model.domain.tiledMicroscope.BoundingBox3d;
+import org.janelia.model.domain.tiledMicroscope.TmWorkspaceInfo;
 import org.janelia.workstation.integration.util.FrameworkAccess;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -153,6 +154,11 @@ public Collection<BoundingBox3d> getWorkspaceBoundingBoxes(Long workspaceId) thr
         return client.getWorkspaceBoundingBoxes(workspaceId);
     }
 
+    public  List<TmWorkspaceInfo> getLargestWorkspaces () {
+        LOG.debug("getLargestWorkspaces()");
+        return client.getLargestWorkspaces(AccessManager.getSubjectKey());
+    }
+
     public List<TmOperation> getOperationLogs (Long workspaceId, Long neuronId, Date startTime, Date endTime,
                                                String subjectKey) {
         LOG.debug("getOperationLogs(workspaceId={}, neuronId={}, startTime={}, endTime={})",
@@ -231,6 +237,11 @@ public void remove(TmWorkspace workspace) throws Exception {
         getModel().notifyDomainObjectRemoved(workspace);
     }
 
+    public void removeWorkspaces(List<Long> selectedWorkspaces) {
+        LOG.debug("removeWorkspaces({})", selectedWorkspaces);
+        client.removeWorkspaces(selectedWorkspaces);
+    }
+
     class RetrieveNeuronsTask extends RecursiveTask<Stream<TmNeuronMetadata>> {
         double defaultLength = 50000.0;
         int start;
diff --git a/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeRestClient.java b/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeRestClient.java
index 217903c64..eb338b110 100644
--- a/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeRestClient.java
+++ b/modules/ViewerController/src/main/java/org/janelia/workstation/controller/access/TiledMicroscopeRestClient.java
@@ -15,6 +15,7 @@
 
 import com.fasterxml.jackson.core.JsonFactory;
 import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.io.ByteStreams;
 
@@ -118,6 +119,27 @@ public TmSample create(TmSample tmSample, Map<String, Object> storageAttributes)
         return response.readEntity(TmSample.class);
     }
 
+    public List<TmWorkspaceInfo> getLargestWorkspaces(String subjectKey ) {
+        WebTarget target =  getMouselightDataEndpoint("/workspace/largest")
+                .queryParam("username", subjectKey);
+        Response response = target
+                .request("application/json")
+                .get();
+        checkBadResponse(target, response);
+        try {
+            String jsonResponse = response.readEntity(String.class);
+
+
+            ObjectMapper objectMapper = new ObjectMapper();
+            return objectMapper.readValue(jsonResponse, new TypeReference<List<TmWorkspaceInfo>>() {
+            });
+        } catch (Exception e) {
+            FrameworkAccess.handleException(e);
+            LOG.error ("Problems returning the largest workspaces in the db");
+            throw new RemoteServiceException("Client had problems retrieving largest workspaces");
+        }
+    }
+
     public List<TmOperation> getOperationLogs(Long workspaceId, Long neuronId,
                                    Date startTime, Date endTime,
                                    String subjectKey ) {
@@ -501,4 +523,13 @@ public boolean isServerPathAvailable(String serverPath, boolean directoryOnly, M
         int responseStatus = response.getStatus();
         return responseStatus == 200;
     }
+
+    public void removeWorkspaces(List<Long> selectedWorkspaces) {
+        WebTarget target = getMouselightDataEndpoint("/workspaces/remove");
+
+        Response response = target
+                .request("application/json")
+                .put(Entity.json(selectedWorkspaces));
+        checkBadResponse(target, response);
+    }
 }
diff --git a/pom.xml b/pom.xml
index 1b55413d4..f2a949e61 100644
--- a/pom.xml
+++ b/pom.xml
@@ -109,7 +109,7 @@
 
         <janeliaws.jetty.version>9.4.46.v20220331</janeliaws.jetty.version>
 
-        <janeliaws.jacs-model.version>3.3.0</janeliaws.jacs-model.version>
+        <janeliaws.jacs-model.version>3.3.4</janeliaws.jacs-model.version>
 
         <janeliaws.jacs-messaging.version>2.5.0</janeliaws.jacs-messaging.version>
 

From ab0b6eea10935ba8b6aa026e6d78c4ce384436d0 Mon Sep 17 00:00:00 2001
From: schauderd <schauderd@janelia.hhmi.org>
Date: Tue, 4 Mar 2025 12:30:59 -0500
Subject: [PATCH 2/2] moved table model reset

---
 .../org/janelia/workstation/admin/DatabaseCleanupPanel.java    | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java b/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java
index 5fd3922f7..9e921d507 100644
--- a/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java
+++ b/modules/AdministrationGUI/src/main/java/org/janelia/workstation/admin/DatabaseCleanupPanel.java
@@ -64,14 +64,13 @@ private void loadLargestWorkspaces() {
 
             @Override
             protected void doStuff() {
-                SwingUtilities.invokeLater(() -> tableModel.clear());
-
                 TiledMicroscopeDomainMgr domainMgr = TiledMicroscopeDomainMgr.getDomainMgr();
                 workspaceResults = domainMgr.getLargestWorkspaces();
             }
 
             @Override
             protected void hadSuccess() {
+                tableModel.clear();
                 tableModel.setWorkspaces(workspaceResults);
             }