Settings: ignored INSTCODEs

anno-gui/src/main/java/org/genesys2/anno/gui/AppWindow.java

@@ -82,6 +82,7 @@ import org.genesys2.anno.model.ColumnDef;
 import org.genesys2.anno.model.Settings;
 import org.json.JSONException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.AnnotationConfigApplicationContext;
@@ -109,6 +110,9 @@ public class AppWindow {
 
 	@Autowired
 	private Settings settings;
+	
+	@Value("${genesys.magic.workspace}")
+	protected String workspacePath;
 
 	private ExecutorService threadPool = Executors.newFixedThreadPool(4);
 
@@ -305,6 +309,12 @@ public class AppWindow {
 		createContents();
 		shlGenesysMagic.open();
 		shlGenesysMagic.layout();
+		try {
+			System.err.println("Trying to load props");
+			settings.load(workspacePath + "/local.properties");
+		} catch (IOException e) {
+			System.err.println("Failed to load props: " + e.getMessage());
+		}
 
 		while (!shlGenesysMagic.isDisposed()) {
 			if (!display.readAndDispatch()) {

anno-gui/src/main/java/org/genesys2/anno/gui/PushDialog.java

@@ -432,6 +432,8 @@ public class PushDialog extends Dialog {
 
 							if (count % 100 == 0)
 								_log.debug("Examining data at row " + count);
+							final Set<String> instCodesFilter = settings.getInstCodeSettings().getInstCodes();
+							final boolean isBlackList = settings.getInstCodeSettings().isBlackList();
 
 							for (Object[] row : rows) {
 								count++;
@@ -442,6 +444,14 @@ public class PushDialog extends Dialog {
 									// Check for instCode
 									accnJson.get(Api1Constants.Accession.INSTCODE).textValue();
 
+									final String accessionInstCode = (String) accnMap.get(RdfMCPD.INSTCODE);
+
+									// If filtering, check INSTCODE is listed
+									if (instCodesFilter.size() > 0 && !(isBlackList ^ instCodesFilter.contains(accessionInstCode))) {
+										_log.info("Ignoring accessions with inst code : " + accessionInstCode);
+										continue;
+									}
+
 								} catch (Throwable e) {
 									_log.info("Error in row " + count + ". " + e.getMessage() + ": " + ArrayUtils.toString(row));
 								}
@@ -618,7 +628,8 @@ public class PushDialog extends Dialog {
 				genesysClient.me();
 
 				// Filter only for specific INSTCODES
-				final Set<String> instCodesFilter = new HashSet<>();
+				final Set<String> instCodesFilter = settings.getInstCodeSettings().getInstCodes();
+				final boolean isBlackList = settings.getInstCodeSettings().isBlackList();
 				_log.warn("Running upload for " + instCodesFilter.toString());
 				
 				
@@ -664,7 +675,8 @@ public class PushDialog extends Dialog {
 								final String accessionInstCode = (String) accnMap.get(RdfMCPD.INSTCODE);
 
 								// If filtering, check INSTCODE is listed
-								if (instCodesFilter.size() > 0 && ! instCodesFilter.contains(accessionInstCode)) {
+								if (instCodesFilter.size() > 0 && !(isBlackList ^ instCodesFilter.contains(accessionInstCode))) {
+									_log.info("Ignoring accessions with inst code : " + accessionInstCode);
 									continue;
 								}
 

anno-gui/src/main/java/org/genesys2/anno/gui/SettingsDialog.java

@@ -26,6 +26,8 @@ import org.eclipse.swt.SWT;
 import org.eclipse.swt.custom.ScrolledComposite;
 import org.eclipse.swt.events.FocusAdapter;
 import org.eclipse.swt.events.FocusEvent;
+import org.eclipse.swt.events.KeyAdapter;
+import org.eclipse.swt.events.KeyEvent;
 import org.eclipse.swt.events.SelectionAdapter;
 import org.eclipse.swt.events.SelectionEvent;
 import org.eclipse.swt.layout.GridData;
@@ -33,14 +35,18 @@ import org.eclipse.swt.layout.GridLayout;
 import org.eclipse.swt.layout.RowLayout;
 import org.eclipse.swt.widgets.Button;
 import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Control;
 import org.eclipse.swt.widgets.Dialog;
 import org.eclipse.swt.widgets.Display;
+import org.eclipse.swt.widgets.Event;
 import org.eclipse.swt.widgets.Group;
 import org.eclipse.swt.widgets.Label;
+import org.eclipse.swt.widgets.Listener;
 import org.eclipse.swt.widgets.Shell;
 import org.eclipse.swt.widgets.TabFolder;
 import org.eclipse.swt.widgets.TabItem;
 import org.eclipse.swt.widgets.Text;
+import org.genesys2.anno.model.InstCodeSettings;
 import org.genesys2.anno.model.OAuthSettings;
 import org.genesys2.anno.model.Settings;
 import org.genesys2.client.oauth.GenesysApiException;
@@ -50,9 +56,12 @@ import org.genesys2.client.oauth.OAuthAuthenticationException;
 import org.genesys2.client.oauth.PleaseRetryException;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import org.springframework.beans.factory.annotation.Value;
 import swing2swt.layout.BorderLayout;
 
+import java.io.IOException;
 import java.util.Arrays;
+import java.util.Set;
 
 public class SettingsDialog extends Dialog {
 
@@ -66,6 +75,9 @@ public class SettingsDialog extends Dialog {
 	private static final Logger _log = Logger.getLogger(SettingsDialog.class);
 	private DataBindingContext m_bindingContext;
 
+	@Value("${genesys.magic.workspace}")
+	protected String workspacePath;
+
 	@Autowired
 	private Settings settings;
 
@@ -80,6 +92,8 @@ public class SettingsDialog extends Dialog {
 	private Text txtClientKey;
 	private Text txtClientSecret;
 	private Text txtScope;
+	private Text txtInstCodesToIgnore;
+	private Composite grpInstCodes;
 
 	/**
 	 * Create the dialog.
@@ -125,6 +139,7 @@ public class SettingsDialog extends Dialog {
 		TabItem tbtmGenesysApi = new TabItem(tabFolder, SWT.NONE);
 		tbtmGenesysApi.setText("Genesys API");
 
+		renderAdvancedSection(tabFolder);
 		ScrolledComposite scrolledComposite = new ScrolledComposite(tabFolder, SWT.V_SCROLL);
 		scrolledComposite.setShowFocusedControl(true);
 		tbtmGenesysApi.setControl(scrolledComposite);
@@ -178,6 +193,150 @@ public class SettingsDialog extends Dialog {
 		m_bindingContext = initDataBindings();
 	}
 
+	private void renderAdvancedSection(TabFolder tabFolder) {
+		InstCodeSettings instCodeSettings = settings.getInstCodeSettings();
+
+		TabItem advancedTab = new TabItem(tabFolder, SWT.NONE);
+		advancedTab.setText("Advanced");
+
+		ScrolledComposite tabContents = new ScrolledComposite(tabFolder, SWT.V_SCROLL);
+		tabContents.setExpandHorizontal(true);
+		tabContents.setShowFocusedControl(true);
+		advancedTab.setControl(tabContents);
+
+		Composite composite = new Composite(tabContents, SWT.NONE);
+		composite.setLayout(new GridLayout(1, false));
+		composite.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false, 2, 1));
+
+		renderAdvancedControllSection(composite);
+
+		Group instCodesGroup = new Group(composite, SWT.BORDER);
+		instCodesGroup.setLayout(new GridLayout());
+		instCodesGroup.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, true));
+		instCodesGroup.setText("Selected institute codes");
+
+		grpInstCodes = new Composite(instCodesGroup, SWT.FILL);
+		grpInstCodes.setLayout(new GridLayout(6, true));
+		grpInstCodes.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, true));
+
+		renderInstCodesList(composite);
+
+		composite.pack();
+		tabContents.setContent(composite);
+		tabContents.setMinSize(composite.computeSize(SWT.FILL, SWT.FILL));
+	}
+
+	private void renderAdvancedControllSection(Composite composite) {
+		InstCodeSettings instCodeSettings = settings.getInstCodeSettings();
+
+		Group controlSection = new Group(composite, SWT.BORDER);
+		controlSection.setLayout(new GridLayout(1, false));
+		controlSection.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false, 1, 1));
+		controlSection.setText("Institute codes filtering");
+
+		Composite radioButtonsComposite = new Composite(controlSection, SWT.NONE);
+		radioButtonsComposite.setLayout(new GridLayout(2, false));
+
+		Button isWhitelistButton = new Button(radioButtonsComposite, SWT.RADIO);
+		isWhitelistButton.addSelectionListener(new SelectionAdapter() {
+			@Override
+			public void widgetSelected(SelectionEvent e) {
+				instCodeSettings.setBlackList(false);
+			}
+		});
+		isWhitelistButton.setSelection(!instCodeSettings.isBlackList());
+		isWhitelistButton.setText("Whitelist");
+
+		Button isBlacklitButton = new Button(radioButtonsComposite, SWT.RADIO);
+		isBlacklitButton.addSelectionListener(new SelectionAdapter() {
+			@Override
+			public void widgetSelected(SelectionEvent e) {
+				instCodeSettings.setBlackList(true);
+			}
+		});
+		isBlacklitButton.setSelection(instCodeSettings.isBlackList());
+		isBlacklitButton.setText("Blacklist");
+
+		Button saveBtn = new Button(composite, SWT.NONE);
+		saveBtn.setLayoutData(new GridData(SWT.END, SWT.CENTER, false, false));
+		saveBtn.addSelectionListener(new SelectionAdapter() {
+			@Override
+			public void widgetSelected(SelectionEvent event) {
+				try {
+					settings.save(workspacePath + "/local.properties");
+				} catch (IOException err) {
+					System.err.println("Failed to load props: " + err.getMessage());
+				}
+			}
+		});
+		saveBtn.setText("Save");
+
+		txtInstCodesToIgnore = new Text(controlSection, SWT.BORDER);
+		txtInstCodesToIgnore.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
+		txtInstCodesToIgnore.setTextLimit(6);
+		txtInstCodesToIgnore.addListener(SWT.FocusOut, new Listener() {
+			@Override
+			public void handleEvent(Event event) {
+				if (!txtInstCodesToIgnore.getText().trim().isEmpty()) {
+					instCodeSettings.getInstCodes().add(txtInstCodesToIgnore.getText().trim());
+					txtInstCodesToIgnore.setText("");
+					renderInstCodesList(composite);
+
+				}
+			}
+		});
+
+		txtInstCodesToIgnore.addKeyListener(new KeyAdapter() {
+			@Override
+			public void keyReleased(KeyEvent e) {
+				final int ENTER_KEY_CODE = 13;
+				if (e.keyCode == ENTER_KEY_CODE && !txtInstCodesToIgnore.getText().trim().isEmpty()) {
+					instCodeSettings.getInstCodes().add(txtInstCodesToIgnore.getText().trim());
+					txtInstCodesToIgnore.setText("");
+					renderInstCodesList(composite);
+
+				}
+			}
+		});
+	}
+
+	private void renderInstCodesList(Composite parent) {
+		InstCodeSettings instCodeSettings = settings.getInstCodeSettings();
+		Set<String> instCodes = instCodeSettings.getInstCodes();
+
+		if (grpInstCodes != null) {
+			for (Control control : grpInstCodes.getChildren()) {
+				control.dispose();
+			}
+		}
+
+		for (String instCode : instCodes) {
+			Group someGroup = new Group(grpInstCodes, SWT.FILL);
+			someGroup.setLayout(new GridLayout(2, false));
+			someGroup.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
+
+			Label lblGenesysServer = new Label(someGroup, SWT.NONE);
+			lblGenesysServer.setLayoutData(new GridData(SWT.BEGINNING, SWT.CENTER, true, false));
+			lblGenesysServer.setText(instCode);
+
+			Button removeInstCodeButton = new Button(someGroup, SWT.PUSH);
+			removeInstCodeButton.setData(instCode);
+			removeInstCodeButton.setLayoutData(new GridData(SWT.END, SWT.CENTER, true, true));
+			removeInstCodeButton.addSelectionListener(new SelectionAdapter() {
+				@Override
+				public void widgetSelected(SelectionEvent e) {
+					instCodes.remove(instCode);
+					renderInstCodesList(parent);
+				}
+			});
+			removeInstCodeButton.setData(instCode);
+			removeInstCodeButton.setText("X");
+		}
+		grpInstCodes.pack();
+		parent.pack();
+		shell.layout(true, true);
+	}
+
 	private void renderServerSection(Group grpGenesysServer, Group grpGenesysApiConfiguration) {
 		OAuthSettings oauthSettings = settings.getOauthSettings();
 

anno-gui/src/main/java/org/genesys2/anno/model/InstCodeSettings.java

+package org.genesys2.anno.model;
+
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Properties;
+import java.util.Set;
+import java.util.TreeSet;
+
+public class InstCodeSettings extends LoadableSettings {
+
+	private static String instCodesPropName = "instCodes";
+	private static String isBlackListPropName = "isBlackList";
+
+	private Set<String> instCodes = new TreeSet<>();
+	private boolean isBlackList = false;
+
+	public Set<String> getInstCodes() {
+		return instCodes;
+	}
+
+	public void setInstCodes(Set<String> instCodes) {
+		firePropertyChange("instCodes", null, this.instCodes);
+		this.instCodes = instCodes;
+	}
+
+	public boolean isBlackList() {
+		return isBlackList;
+	}
+
+	public void setBlackList(boolean blackList) {
+		firePropertyChange("isBlackList", null, this.isBlackList);
+		isBlackList = blackList;
+	}
+
+	@Override
+	public void save(String propFilePath) throws IOException {
+		firePropertyChange("instCodeSettings", null, this);
+
+		Properties prop = new Properties();
+		prop.setProperty(instCodesPropName, this.getInstCodes().toString());
+		prop.setProperty(isBlackListPropName, String.valueOf(this.isBlackList()));
+		prop.store(new FileOutputStream(propFilePath), "Inst codes filtering saved");
+	}
+
+	@Override
+	public LoadableSettings load(String propFilePath) throws IOException {
+		Properties prop = new Properties();
+		prop.load(new FileInputStream(propFilePath));
+
+		if (!prop.isEmpty()) {
+			this.instCodes = new TreeSet<>(Arrays.asList(prop.getProperty(instCodesPropName).replaceAll("[,\\[\\]]", "").split(" +")));
+			this.isBlackList = Boolean.valueOf(prop.getProperty(isBlackListPropName));
+		}
+		firePropertyChange("instCodeSettings", null, this);
+		return this;
+	}
+}

anno-gui/src/main/java/org/genesys2/anno/model/LoadableSettings.java

+package org.genesys2.anno.model;
+
+import org.genesys2.anno.gui.AbstractModelObject;
+
+import java.io.IOException;
+
+public abstract class LoadableSettings extends AbstractModelObject {
+
+	public abstract void save(String propFilePath) throws IOException;
+
+	public abstract LoadableSettings load(String propFilePath) throws IOException;
+}

anno-gui/src/main/java/org/genesys2/anno/model/Settings.java

@@ -15,10 +15,12 @@
  */
 package org.genesys2.anno.model;
 
-import org.genesys2.anno.gui.AbstractModelObject;
+import java.io.IOException;
+
+public class Settings extends LoadableSettings {
 
-public class Settings extends AbstractModelObject {
 	private OAuthSettings oauthSettings = new OAuthSettings();
+	private InstCodeSettings instCodeSettings = new InstCodeSettings();
 
 	public OAuthSettings getOauthSettings() {
 		return oauthSettings;
@@ -28,4 +30,25 @@ public class Settings extends AbstractModelObject {
 		this.oauthSettings = oauthSettings;
 		firePropertyChange("oauthSettings", null, this.oauthSettings);
 	}
+
+	public InstCodeSettings getInstCodeSettings() {
+		return instCodeSettings;
+	}
+
+	public void setInstCodeSettings(InstCodeSettings instCodeSettings) {
+		firePropertyChange("instCodeSettings", null, this.instCodeSettings);
+		this.instCodeSettings = instCodeSettings;
+	}
+
+	@Override
+	public void save(String propFilePath) throws IOException {
+		instCodeSettings.save(propFilePath);
+	}
+
+	@Override
+	public LoadableSettings load(String propFilePath) throws IOException {
+		setInstCodeSettings((InstCodeSettings)instCodeSettings.load(propFilePath));
+
+		return this;
+	}
 }