[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Wed Nov 2 06:39:06 UTC 2005
senger
Wed Nov 2 01:39:06 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory pub.open-bio.org:/tmp/cvs-serv12193/src/main/org/biomoby/service/dashboard
Modified Files:
CommonTree.java DataTypesTree.java NamespacesTree.java
RegistryModel.java RegistryPanel.java ServiceTypesTree.java
Added Files:
ServicesBoard.java ServicesTree.java
Log Message:
moby-live/Java/src/main/org/biomoby/service/dashboard ServicesBoard.java,NONE,1.1 ServicesTree.java,NONE,1.1 CommonTree.java,1.9,1.10 DataTypesTree.java,1.6,1.7 NamespacesTree.java,1.1,1.2 RegistryModel.java,1.11,1.12 RegistryPanel.java,1.15,1.16 ServiceTypesTree.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java 2005/10/28 11:30:37 1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java 2005/11/02 06:39:06 1.10
@@ -55,14 +55,23 @@
protected final static String AC_EXPAND = "ac-expand";
protected final static String AC_COLLAPSE = "ac-collapse";
protected final static String AC_RELOAD = "ac-reload";
+ protected final static String AC_NSORT = "ac-nsort";
+ protected final static String AC_ASORT = "ac-asort";
// some shared constants
- final static protected int SORTED_BY_NAME = 0;
- final static protected int SORTED_BY_AUTHORITY = 1;
+ final static protected int SORTED_BY_NAME = 0;
+ final static protected int SORTED_BY_AUTHORITY = 1;
+ final static protected int SORTED_UNUSUAL = 9;
+ // all higher numbers indicates an unusual sorting order that we
+ // will not keep in case of reloading
+ final static protected int SORTED_BY_SERVICE_TYPE = 11;
+ final static protected int SORTED_BY_INPUT_DATA = 12;
+ final static protected int SORTED_BY_OUTPUT_DATA = 13;
// tree components
protected JPopupMenu popup;
protected String lastSearchText = "";
+ protected int lastSorted = SORTED_BY_NAME;
// shared icons
static protected Icon searchIcon;
@@ -70,6 +79,11 @@
static protected Icon menuExpandIcon, menuExpandIconDis;
static protected Icon menuCollapseIcon, menuCollapseIconDis;
static protected Icon menuReloadIcon, menuReloadIconDis;
+ static protected Icon smallNIcon, smallNIconDis;
+ static protected Icon smallAIcon, smallAIconDis;
+ static protected Icon smallTIcon, smallTIconDis;
+ static protected Icon smallIIcon, smallIIconDis;
+ static protected Icon smallOIcon, smallOIconDis;
protected String rootNode;
@@ -212,6 +226,22 @@
if (menuReloadIconDis == null)
menuReloadIconDis =
SwingUtils.createIcon ("images/smallReload_dis.gif", Dashboard.class);
+
+ if (smallNIcon == null) smallNIcon = loadIcon ("images/smallN.gif");
+ if (smallNIconDis == null) smallNIconDis = loadIcon ("images/smallN_dis.gif");
+ if (smallAIcon == null) smallAIcon = loadIcon ("images/smallA.gif");
+ if (smallAIconDis == null) smallAIconDis = loadIcon ("images/smallA_dis.gif");
+ if (smallTIcon == null) smallTIcon = loadIcon ("images/smallT.gif");
+ if (smallTIconDis == null) smallTIconDis = loadIcon ("images/smallT_dis.gif");
+ if (smallIIcon == null) smallIIcon = loadIcon ("images/smallI.gif");
+ if (smallIIconDis == null) smallIIconDis = loadIcon ("images/smallI_dis.gif");
+ if (smallOIcon == null) smallOIcon = loadIcon ("images/smallO.gif");
+ if (smallOIconDis == null) smallOIconDis = loadIcon ("images/smallO_dis.gif");
+ }
+
+ //
+ private Icon loadIcon (String path) {
+ return SwingUtils.createIcon (path, Dashboard.class);
}
/*********************************************************************
@@ -312,6 +342,25 @@
}
/*********************************************************************
+ * Adding sorting items to the popup menu.
+ ********************************************************************/
+ protected void addSortingItems() {
+ popup.addSeparator();
+ popup.add
+ (createMenuItem (new AbstractAction ("Sort by names") {
+ public void actionPerformed (ActionEvent e) {
+ update (lastSorted = SORTED_BY_NAME, null);
+ }
+ }, AC_NSORT, smallNIcon, smallNIconDis));
+ popup.add
+ (createMenuItem (new AbstractAction ("Sort by authorities") {
+ public void actionPerformed (ActionEvent e) {
+ update (lastSorted = SORTED_BY_AUTHORITY, null);
+ }
+ }, AC_ASORT, smallAIcon, smallAIconDis));
+ }
+
+ /*********************************************************************
* Collapse all nodes, starting from the root. <p>
********************************************************************/
protected void collapse() {
@@ -389,7 +438,8 @@
Enumeration en = root.depthFirstEnumeration();
while (en.hasMoreElements()) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode)en.nextElement();
- if (toBeHighlighted.contains (node.getUserObject().toString())) {
+// if (toBeHighlighted.contains (node.getUserObject().toString())) {
+ if (toBeHighlighted.contains ( ((CommonNode)node.getUserObject()).getValue())) {
makeVisible (new TreePath (tModel.getPathToRoot (node)));
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesTree.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesTree.java 2005/10/28 11:30:37 1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesTree.java 2005/11/02 06:39:06 1.7
@@ -46,8 +46,6 @@
org.apache.commons.logging.LogFactory.getLog (DataTypesTree.class);
// action commands for popup menu items
- protected final static String AC_NSORT = "ac-nsort";
- protected final static String AC_ASORT = "ac-asort";
protected final static String AC_HASA = "ac-hasa";
protected final static String AC_DEPR = "ac-depr";
@@ -56,7 +54,6 @@
CommonConsole console;
MobyDataType[] dataTypes = null;
- int lastSorted = SORTED_BY_NAME;
boolean showBadGuys = false;
boolean showMembers = false;
JCheckBoxMenuItem deprecatedBox;
@@ -83,21 +80,7 @@
********************************************************************/
protected void createPopups (String title) {
super.createPopups (title);
- popup.addSeparator();
- popup.add
- (createMenuItem (new AbstractAction ("Sort by names") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_NAME, null);
- deprecatedBox.setEnabled (true);
- }
- }, AC_NSORT));
- popup.add
- (createMenuItem (new AbstractAction ("Sort by authorities") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_AUTHORITY, null);
- deprecatedBox.setEnabled (false);
- }
- }, AC_ASORT));
+ addSortingItems();
popup.addSeparator();
JCheckBoxMenuItem showBox = new JCheckBoxMenuItem ("Show HAS/HASA members");
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NamespacesTree.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NamespacesTree.java 2005/10/28 13:39:09 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NamespacesTree.java 2005/11/02 06:39:06 1.2
@@ -45,16 +45,11 @@
private static org.apache.commons.logging.Log log =
org.apache.commons.logging.LogFactory.getLog (NamespacesTree.class);
- // action commands for popup menu items
- protected final static String AC_NSORT = "ac-nsort";
- protected final static String AC_ASORT = "ac-asort";
-
// remembered from constructor
RegistryModel registryModel;
CommonConsole console;
MobyNamespace[] namespaces = null;
- int lastSorted = SORTED_BY_NAME;
MobyException updateException = null;
final static String NAMESPACES_ACCESS_ERROR =
@@ -73,24 +68,11 @@
}
/*********************************************************************
- * Adding data types tree specific menu items to a
- * right-click-popup.
+ *
********************************************************************/
protected void createPopups (String title) {
super.createPopups (title);
- popup.addSeparator();
- popup.add
- (createMenuItem (new AbstractAction ("Sort by names") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_NAME, null);
- }
- }, AC_NSORT));
- popup.add
- (createMenuItem (new AbstractAction ("Sort by authorities") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_AUTHORITY, null);
- }
- }, AC_ASORT));
+ addSortingItems();
}
/*********************************************************************
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java 2005/10/28 13:39:09 1.11
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java 2005/11/02 06:39:06 1.12
@@ -13,6 +13,7 @@
import org.biomoby.shared.NoSuccessException;
import org.biomoby.shared.MobyDataType;
import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.MobyService;
import org.biomoby.shared.MobyNamespace;
import org.biomoby.shared.CentralAll;
import org.biomoby.client.CentralDigestCachedImpl;
@@ -46,6 +47,7 @@
Hashtable dataTypesTable = new Hashtable();
Hashtable serviceTypesTable = new Hashtable();
Hashtable namespacesTable = new Hashtable();
+ Hashtable servicesTable = new Hashtable();
private static final String MSG_REG_PENDING_CURATION =
"Registration reports 'Pending curation'...\n" +
@@ -183,13 +185,13 @@
public void registerServiceType (MobyServiceType serviceType)
throws MobyException {
initWorker();
- try {
- worker.registerServiceType (serviceType);
- } catch (PendingCurationException e) {
- throw new MobyException (MSG_REG_PENDING_CURATION);
- } catch (NoSuccessException e) {
- throw new MobyException (MSG_REG_NO_SUCCESS + e.getMessage());
- }
+// try {
+// worker.registerServiceType (serviceType);
+// } catch (PendingCurationException e) {
+// throw new MobyException (MSG_REG_PENDING_CURATION);
+// } catch (NoSuccessException e) {
+// throw new MobyException (MSG_REG_NO_SUCCESS + e.getMessage());
+// }
}
/*********************************************************************
@@ -198,13 +200,13 @@
public void unRegisterServiceType (MobyServiceType serviceType)
throws MobyException {
initWorker();
- try {
- worker.unregisterServiceType (serviceType);
- } catch (PendingCurationException e) {
- throw new MobyException (MSG_UNREG_PENDING_CURATION);
- } catch (NoSuccessException e) {
- throw new MobyException (MSG_UNREG_NO_SUCCESS + e.getMessage());
- }
+// try {
+// worker.unregisterServiceType (serviceType);
+// } catch (PendingCurationException e) {
+// throw new MobyException (MSG_UNREG_PENDING_CURATION);
+// } catch (NoSuccessException e) {
+// throw new MobyException (MSG_UNREG_NO_SUCCESS + e.getMessage());
+// }
}
/*********************************************************************
@@ -269,13 +271,13 @@
public void registerNamespace (MobyNamespace namespace)
throws MobyException {
initWorker();
- try {
- worker.registerNamespace (namespace);
- } catch (PendingCurationException e) {
- throw new MobyException (MSG_REG_PENDING_CURATION);
- } catch (NoSuccessException e) {
- throw new MobyException (MSG_REG_NO_SUCCESS + e.getMessage());
- }
+// try {
+// worker.registerNamespace (namespace);
+// } catch (PendingCurationException e) {
+// throw new MobyException (MSG_REG_PENDING_CURATION);
+// } catch (NoSuccessException e) {
+// throw new MobyException (MSG_REG_NO_SUCCESS + e.getMessage());
+// }
}
/*********************************************************************
@@ -284,13 +286,13 @@
public void unRegisterNamespace (MobyNamespace namespace)
throws MobyException {
initWorker();
- try {
- worker.unregisterNamespace (namespace);
- } catch (PendingCurationException e) {
- throw new MobyException (MSG_UNREG_PENDING_CURATION);
- } catch (NoSuccessException e) {
- throw new MobyException (MSG_UNREG_NO_SUCCESS + e.getMessage());
- }
+// try {
+// worker.unregisterNamespace (namespace);
+// } catch (PendingCurationException e) {
+// throw new MobyException (MSG_UNREG_PENDING_CURATION);
+// } catch (NoSuccessException e) {
+// throw new MobyException (MSG_UNREG_NO_SUCCESS + e.getMessage());
+// }
}
/*********************************************************************
@@ -345,6 +347,94 @@
/*********************************************************************
*
+ * Dealing with Moby Services.
+ *
+ ********************************************************************/
+
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public void registerService (MobyService service)
+ throws MobyException {
+ initWorker();
+// try {
+// worker.registerService (service);
+// } catch (PendingCurationException e) {
+// throw new MobyException (MSG_REG_PENDING_CURATION);
+// } catch (NoSuccessException e) {
+// throw new MobyException (MSG_REG_NO_SUCCESS + e.getMessage());
+// }
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public void unRegisterService (MobyService service)
+ throws MobyException {
+ initWorker();
+// try {
+// worker.unregisterService (service);
+// } catch (PendingCurationException e) {
+// throw new MobyException (MSG_UNREG_PENDING_CURATION);
+// } catch (NoSuccessException e) {
+// throw new MobyException (MSG_UNREG_NO_SUCCESS + e.getMessage());
+// }
+ }
+
+ /*********************************************************************
+ * Fetch services (from a cache or from a registry). When done,
+ * signal that services are updated. If an initiator is known (not
+ * null), signal, who asked for it, as well.
+ ********************************************************************/
+ public synchronized MobyService[] getServices (Object initiator)
+ throws MobyException {
+ initWorker();
+ if (initiator != null)
+ fireEvent (initiator, AUTHORITIES_RESET, "", null);
+ MobyService[] services = worker.getServices();
+ servicesTable = new Hashtable();
+ for (int i = 0; i < services.length; i++)
+ servicesTable.put (services[i].getUniqueName(),
+ services[i]);
+ if (initiator != null)
+ fireEvent (initiator, AUTHORITIES_UPDATED, "", services);
+ return services;
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public MobyService getService (String combinedServiceName)
+ throws MobyException {
+ if (combinedServiceName == null)
+ return null;
+ MobyService[] services = getServices (null);
+ return (MobyService)servicesTable.get (combinedServiceName);
+ }
+
+ /*********************************************************************
+ * Return a HashSet filled with names of services that have
+ * somewhere given 'searchText'. Add case-insensitivity to the
+ * regular expression in 'searchText'.
+ ********************************************************************/
+ public HashSet findInServices (String searchText)
+ throws MobyException {
+ HashSet found = new HashSet();
+ MobyService[] services = getServices (null);
+ if (! searchText.startsWith ("(?i)"))
+ searchText = "(?i)" + searchText;
+ Pattern pattern = Pattern.compile (searchText);
+ for (int i = 0; i < services.length; i++) {
+ if (pattern.matcher (services[i].toString()).find())
+ found.add (services[i].getUniqueName());
+ }
+ return found;
+ }
+
+
+ /*********************************************************************
+ *
* The rest...
*
********************************************************************/
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java 2005/10/28 13:39:09 1.15
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java 2005/11/02 06:39:06 1.16
@@ -119,7 +119,6 @@
console.setAppendMode (false);
// ontology trees
- ServicesTree servicesTree = new ServicesTree();
DataTypesBoard dataTypesBoard =
new DataTypesBoard (registryModel,
console,
@@ -135,9 +134,15 @@
console,
propertyChannel);
namespacesBoard.updateTree (CommonTree.SORTED_BY_NAME);
+ ServicesBoard servicesBoard =
+ new ServicesBoard (registryModel,
+ console,
+ propertyChannel);
+ servicesBoard.updateTree (CommonTree.SORTED_BY_NAME);
+ // split it into moving panels
JSplitPane split1 = new JSplitPane (JSplitPane.HORIZONTAL_SPLIT,
- servicesTree.scrollable(),
+ servicesBoard,
dataTypesBoard);
split1.setResizeWeight (0.5);
split1.setContinuousLayout (true);
@@ -318,35 +323,6 @@
/**************************************************************************
*
**************************************************************************/
- class ServicesTree extends CommonTree {
- public ServicesTree() {
- super ("Services");
- }
- }
-
-
- /**************************************************************************
- *
- **************************************************************************/
- class ServiceTypesTree extends CommonTree {
- public ServiceTypesTree() {
- super ("Service Types");
- }
- }
-
-
- /**************************************************************************
- *
- **************************************************************************/
- class NamespacesTree extends CommonTree {
- public NamespacesTree() {
- super ("Namespaces");
- }
- }
-
- /**************************************************************************
- *
- **************************************************************************/
public String getName() {
return "Registry Browser";
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceTypesTree.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceTypesTree.java 2005/10/28 13:39:09 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/ServiceTypesTree.java 2005/11/02 06:39:06 1.3
@@ -46,16 +46,11 @@
private static org.apache.commons.logging.Log log =
org.apache.commons.logging.LogFactory.getLog (ServiceTypesTree.class);
- // action commands for popup menu items
- protected final static String AC_NSORT = "ac-nsort";
- protected final static String AC_ASORT = "ac-asort";
-
// remembered from constructor
RegistryModel registryModel;
CommonConsole console;
MobyServiceType[] serviceTypes = null;
- int lastSorted = SORTED_BY_NAME;
MobyException updateException = null;
final static String SERVICE_TYPES_ACCESS_ERROR =
@@ -74,24 +69,11 @@
}
/*********************************************************************
- * Adding data types tree specific menu items to a
- * right-click-popup.
+ *
********************************************************************/
protected void createPopups (String title) {
super.createPopups (title);
- popup.addSeparator();
- popup.add
- (createMenuItem (new AbstractAction ("Sort by names") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_NAME, null);
- }
- }, AC_NSORT));
- popup.add
- (createMenuItem (new AbstractAction ("Sort by authorities") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_AUTHORITY, null);
- }
- }, AC_ASORT));
+ addSortingItems();
}
/*********************************************************************
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