[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Fri Oct 28 11:30:37 UTC 2005
senger
Fri Oct 28 07:30:37 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory pub.open-bio.org:/tmp/cvs-serv13398/src/main/org/biomoby/service/dashboard
Modified Files:
CommonBoard.java CommonTree.java Dashboard.java
DataTypesBoard.java DataTypesTree.java NOTES
PropertyChannel.java RegistryModel.java RegistryPanel.java
Added Files:
ServiceTypesBoard.java ServiceTypesTree.java
Log Message:
moby-live/Java/src/main/org/biomoby/service/dashboard ServiceTypesBoard.java,NONE,1.1 ServiceTypesTree.java,NONE,1.1 CommonBoard.java,1.3,1.4 CommonTree.java,1.8,1.9 Dashboard.java,1.9,1.10 DataTypesBoard.java,1.4,1.5 DataTypesTree.java,1.5,1.6 NOTES,1.12,1.13 PropertyChannel.java,1.5,1.6 RegistryModel.java,1.9,1.10 RegistryPanel.java,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonBoard.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonBoard.java 2005/10/28 07:58:08 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonBoard.java 2005/10/28 11:30:37 1.4
@@ -43,7 +43,7 @@
implements NotificationListener {
private static org.apache.commons.logging.Log log =
- org.apache.commons.logging.LogFactory.getLog (RegistryModel.class);
+ org.apache.commons.logging.LogFactory.getLog (CommonBoard.class);
protected RegistryModel model;
protected PropertyChannel channel;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java 2005/10/28 07:58:08 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java 2005/10/28 11:30:37 1.9
@@ -73,6 +73,12 @@
protected String rootNode;
+ final static protected String ACCESS_ERROR_INTRO =
+ "Check please values in text fields (in Registry Browser)\n"
+ + "specifying registry endpoint and namespace, and in the\n"
+ + "one specifying directory used as a local cache. Then\n"
+ + "right-click in the data types area and select 'Reload'.\n\n";
+
/*********************************************************************
* Constructor
********************************************************************/
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/Dashboard.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/Dashboard.java 2005/10/28 07:58:08 1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/Dashboard.java 2005/10/28 11:30:37 1.10
@@ -52,7 +52,7 @@
implements DashboardPanel, ChangeListener {
private static org.apache.commons.logging.Log log =
- org.apache.commons.logging.LogFactory.getLog (RegistryModel.class);
+ org.apache.commons.logging.LogFactory.getLog (Dashboard.class);
private JComponent dashboard;
private DashboardHeader header;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesBoard.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesBoard.java 2005/10/28 07:58:08 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesBoard.java 2005/10/28 11:30:37 1.5
@@ -29,7 +29,7 @@
extends CommonBoard {
private static org.apache.commons.logging.Log log =
- org.apache.commons.logging.LogFactory.getLog (RegistryModel.class);
+ org.apache.commons.logging.LogFactory.getLog (DataTypesBoard.class);
/*********************************************************************
* Constructor. <p>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesTree.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesTree.java 2005/10/28 07:58:08 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/DataTypesTree.java 2005/10/28 11:30:37 1.6
@@ -43,7 +43,7 @@
extends CommonTree {
private static org.apache.commons.logging.Log log =
- org.apache.commons.logging.LogFactory.getLog (RegistryModel.class);
+ org.apache.commons.logging.LogFactory.getLog (DataTypesTree.class);
// action commands for popup menu items
protected final static String AC_NSORT = "ac-nsort";
@@ -64,17 +64,14 @@
final static String DATA_TYPES_ACCESS_ERROR =
"An error happened when accessing a list of available data types.\n\n"
- + "Check please values in text fields (in Registry Browser)\n"
- + "specifying registry endpoint and namespace, and in the\n"
- + "one specifying directory used as a local cache. Then\n"
- + "right-click in the data types area and select 'Reload'.\n\n";
+ + ACCESS_ERROR_INTRO;
/*********************************************************************
* Constructor.
********************************************************************/
public DataTypesTree (RegistryModel registryModel,
CommonConsole console) {
- super ("DataTypes");
+ super ("Data Types");
this.registryModel = registryModel;
this.console = console;
createPopups ("Data Types Menu");
@@ -309,7 +306,7 @@
public Object construct() {
try {
if (UUtils.notEmpty (regex))
- found = registryModel.find (regex);
+ found = registryModel.findInDataTypes (regex);
} catch (MobyException e) {
error (DATA_TYPES_ACCESS_ERROR, e);
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NOTES,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NOTES 2005/10/28 07:58:08 1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NOTES 2005/10/28 11:30:37 1.13
@@ -1,3 +1,8 @@
+* BUG: When 'no-use-chache' then changing sorting also reloads; which
+ is bad I think
+
+* Reload ... does it ignore cache?
+
TODO generally:
---------------
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PropertyChannel.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PropertyChannel.java 2005/10/27 08:55:48 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PropertyChannel.java 2005/10/28 11:30:37 1.6
@@ -10,9 +10,6 @@
import org.tulsoft.shared.UUtils;
-import org.apache.commons.logging.LogFactory;
-import org.apache.commons.logging.Log;
-
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeSupport;
@@ -62,7 +59,9 @@
public class PropertyChannel
extends Hashtable {
- private static Log log = LogFactory.getLog (PropertyChannel.class);
+ private static org.apache.commons.logging.Log log =
+ org.apache.commons.logging.LogFactory.getLog (PropertyChannel.class);
+
private PropertyChangeSupport support;
/*********************************************************************
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.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/RegistryModel.java 2005/10/28 07:58:08 1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java 2005/10/28 11:30:37 1.10
@@ -12,6 +12,7 @@
import org.biomoby.shared.PendingCurationException;
import org.biomoby.shared.NoSuccessException;
import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyServiceType;
import org.biomoby.shared.CentralAll;
import org.biomoby.client.CentralDigestCachedImpl;
@@ -41,7 +42,22 @@
CentralAll worker;
boolean useCache = true;
- Hashtable dataTypesTable;
+ Hashtable dataTypesTable = new Hashtable();
+ Hashtable serviceTypesTable = new Hashtable();
+
+ private static final String MSG_REG_PENDING_CURATION =
+ "Registration reports 'Pending curation'...\n" +
+ "Well, nobody knows what it means. Call Mark!";
+
+ private static final String MSG_REG_NO_SUCCESS =
+ "Registration reports 'No Success'...\n";
+
+ private static final String MSG_UNREG_PENDING_CURATION =
+ "Unregistration reports 'Pending curation'...\n" +
+ "Well, nobody knows what it means. Call Mark!";
+
+ private static final String MSG_UNREG_NO_SUCCESS =
+ "Unregistration reports 'No Success'...\n";
/*********************************************************************
* Default constructor.
@@ -65,6 +81,13 @@
return CentralDigestCachedImpl.DEFAULT_NAMESPACE;
}
+
+ /*********************************************************************
+ *
+ * Dealing with Moby Data Types.
+ *
+ ********************************************************************/
+
/*********************************************************************
*
********************************************************************/
@@ -74,11 +97,9 @@
// try {
// worker.registerDataType (dataType);
// } catch (PendingCurationException e) {
-// throw new MobyException ("Registration reports 'Pending curation'...\n" +
-// "Well, nobody knows what it means. Call Mark!");
+// throw new MobyException (MSG_REG_PENDING_CURATION);
// } catch (NoSuccessException e) {
-// throw new MobyException ("Registration reports 'No Success'...\n" +
-// e.getMessage());
+// throw new MobyException (MSG_REG_NO_SUCCESS + e.getMessage());
// }
}
@@ -91,18 +112,16 @@
// try {
// worker.unregisterDataType (dataType);
// } catch (PendingCurationException e) {
-// throw new MobyException ("Unregistration reports 'Pending curation'...\n" +
-// "Well, nobody knows what it means. Call Mark!");
+// throw new MobyException (MSG_UNREG_PENDING_CURATION);
// } catch (NoSuccessException e) {
-// throw new MobyException ("Unregistration reports 'No Success'...\n" +
-// e.getMessage());
+// throw new MobyException (MSG_UNREG_NO_SUCCESS + e.getMessage());
// }
}
/*********************************************************************
* Fetch data types (from a cache or from a registry). When done,
- * signal that data type are updated. If an initiator is known
- * (not null), signal, who asked for data, as well.
+ * signal that data types are updated. If an initiator is known
+ * (not null), signal, who asked for it, as well.
********************************************************************/
public synchronized MobyDataType[] getDataTypes (Object initiator)
throws MobyException {
@@ -110,6 +129,9 @@
if (initiator != null)
fireEvent (initiator, DATA_TYPES_RESET, "", null);
MobyDataType[] dataTypes = worker.getDataTypes();
+ dataTypesTable.clear();
+ for (int i = 0; i < dataTypes.length; i++)
+ dataTypesTable.put (dataTypes[i].getName(), dataTypes[i]);
if (initiator != null)
fireEvent (initiator, DATA_TYPES_UPDATED, "", dataTypes);
return dataTypes;
@@ -122,15 +144,7 @@
throws MobyException {
if (dataTypeName == null)
return null;
-
MobyDataType[] dataTypes = getDataTypes (null);
-
- if (dataTypesTable == null) {
- dataTypesTable = new Hashtable();
- for (int i = 0; i < dataTypes.length; i++) {
- dataTypesTable.put (dataTypes[i].getName(), dataTypes[i]);
- }
- }
return (MobyDataType)dataTypesTable.get (dataTypeName);
}
@@ -139,7 +153,7 @@
* somewhere given 'searchText'. Add case-insensitivity to the
* regular expression in 'searchText'.
********************************************************************/
- public HashSet find (String searchText)
+ public HashSet findInDataTypes (String searchText)
throws MobyException {
HashSet found = new HashSet();
MobyDataType[] dataTypes = getDataTypes (null);
@@ -153,6 +167,100 @@
return found;
}
+
+ /*********************************************************************
+ *
+ * Dealing with Moby Service Types.
+ *
+ ********************************************************************/
+
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ 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());
+ }
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ 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());
+ }
+ }
+
+ /*********************************************************************
+ * Fetch service types (from a cache or from a registry). When done,
+ * signal that service types are updated. If an initiator is known
+ * (not null), signal, who asked for it, as well.
+ ********************************************************************/
+ public synchronized MobyServiceType[] getServiceTypes (Object initiator)
+ throws MobyException {
+ initWorker();
+ if (initiator != null)
+ fireEvent (initiator, SERVICE_TYPES_RESET, "", null);
+ MobyServiceType[] serviceTypes = worker.getFullServiceTypes();
+ serviceTypesTable = new Hashtable();
+ for (int i = 0; i < serviceTypes.length; i++)
+ serviceTypesTable.put (serviceTypes[i].getName(), serviceTypes[i]);
+ if (initiator != null)
+ fireEvent (initiator, SERVICE_TYPES_UPDATED, "", serviceTypes);
+ return serviceTypes;
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public MobyServiceType getServiceType (String serviceTypeName)
+ throws MobyException {
+ if (serviceTypeName == null)
+ return null;
+ MobyServiceType[] serviceTypes = getServiceTypes (null);
+ return (MobyServiceType)serviceTypesTable.get (serviceTypeName);
+ }
+
+ /*********************************************************************
+ * Return a HashSet filled with names of service types that have
+ * somewhere given 'searchText'. Add case-insensitivity to the
+ * regular expression in 'searchText'.
+ ********************************************************************/
+ public HashSet findInServiceTypes (String searchText)
+ throws MobyException {
+ HashSet found = new HashSet();
+ MobyServiceType[] serviceTypes = getServiceTypes (null);
+ if (! searchText.startsWith ("(?i)"))
+ searchText = "(?i)" + searchText;
+ Pattern pattern = Pattern.compile (searchText);
+ for (int i = 0; i < serviceTypes.length; i++) {
+ if (pattern.matcher (serviceTypes[i].toString()).find())
+ found.add (serviceTypes[i].getName());
+ }
+ return found;
+ }
+
+
+ /*********************************************************************
+ *
+ * The rest...
+ *
+ ********************************************************************/
+
/*********************************************************************
*
********************************************************************/
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java 2005/10/27 08:55:48 1.13
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java 2005/10/28 11:30:37 1.14
@@ -11,6 +11,7 @@
import org.biomoby.shared.MobyException;
import org.biomoby.shared.Central;
import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyServiceType;
import org.biomoby.shared.MobyRelationship;
import org.biomoby.service.generator.DataTypesGenerator;
@@ -118,12 +119,17 @@
// ontology trees
ServicesTree servicesTree = new ServicesTree();
- ServiceTypesTree serviceTypesTree = new ServiceTypesTree();
NamespacesTree namespacesTree = new NamespacesTree();
- DataTypesBoard dataTypesBoard = new DataTypesBoard (registryModel,
- console,
- propertyChannel);
+ DataTypesBoard dataTypesBoard =
+ new DataTypesBoard (registryModel,
+ console,
+ propertyChannel);
dataTypesBoard.updateTree (CommonTree.SORTED_BY_NAME);
+ ServiceTypesBoard serviceTypesBoard =
+ new ServiceTypesBoard (registryModel,
+ console,
+ propertyChannel);
+ serviceTypesBoard.updateTree (CommonTree.SORTED_BY_NAME);
JSplitPane split1 = new JSplitPane (JSplitPane.HORIZONTAL_SPLIT,
servicesTree.scrollable(),
@@ -133,7 +139,7 @@
split1.setOneTouchExpandable (true);
JSplitPane split2 = new JSplitPane (JSplitPane.HORIZONTAL_SPLIT,
- serviceTypesTree.scrollable(),
+ serviceTypesBoard,
namespacesTree.scrollable());
split2.setResizeWeight (0.5);
split2.setContinuousLayout (true);
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