Wandora

Hello,

I discoverd Wandora and it is a really powerfull tool.

But I think I'm facing an issue on the 2014-05-05 built wandora release : I'm not able to load the all objects I created in a project I created and saved. Only one topics appears in the "Topics" pannel.
Only one part of the "tree" I created is loading.
My project contains topics and assoc.

FYI :
The "Finder" pannel found existing topic I seached : [null]
Instead of none existing topic search resulting as : /_\ Found no topics !


When I try to :
File > Open Project > "My Project.wpr"

Here is the cmd output :
Importing XTM (2.0) topic map.
Found 26 topics, 48 associations and 12 occurrences.
Restoring consistency check to 'true'.

Can you please revert on this ?
Best Regards.
D. S.

Hello Damien

Thinking of what you wrote in your post, it looks to me that the project you saved contains only Wandora's base ontology i.e. topics and associations that Wandora loads automatically when the application starts. Did you really create more topics and associations in the topic map addition to the default ones before you saved the project?

You can try this small test:

* Restart Wandora application.
* Bottom-right corner contains now two numbers beside the layer name. You should see "Base (26,48)" meaning the Base layer contains 26 topics and 48 associations.
* Select topic Wandora class in the topics panel.
* Right click the Wandora class topic and select menu option New topic... . A create new topic dialog should open.
* Write "test" to the Base name field and press Create button. Wandora informs it has added default subject identifier to the test topic. Ok.
* Now you should see the test in the topics panel. Also note, the topic count number has increased by one.
* Select menu option File > Save project. Give a unique filename for the project. Notice the folder in which Wandora saves the project.
* Restart Wandora application.
* Check the topic and association counts are again 26 and 48. Can't see the test topic anymore.
* Select menu option File > Open project.
* Locate the project you saved few steps ago.
* Load the project.
* Now, if everything went ok, you should see the test topic again in the topics panel and topic count is 27.

Tell, what happened.

The finder panel uses regular expressions. Thus, searching for [null] (with explicit brackets) should return all topics.

Just one more thing. I have been assuming you are using a memory topic map [1]. But are you? The picture would be more understandable, if you are playing with database layers [2].

Kind Regards,
Aki / Wandora Team


[1] http://wandora.org/wiki/Memory_topic_map
[2] http://wandora.org/wiki/Database_topic_map

Hello Aki,

Thanks for your quick answer.

* I'm sure to having saved my projects with new topics and associations.

* Regarding the small test : After having completed all steps, I confirmed the expected result : Base(27,48)
Now, if I load my project, I see Base(53,82)

* To be honest, I had no information on layers before you talk about it in your answer. I'll take a look on this.

* I tried to search [null] in the finder panel, It returns (it's random on each loading I've done) 2 or 3 lines max :
1- "[null]"
2- "My Root Project topic"
3- (sometimes) a random topic I created.

One more think I've done that maybe had corrupted the project :
To have clean environement, I had deleted all wandora topics until the root "Wandora class" topic, then, I created my topics.

Regards.
Damien.

Hello Damien

Great, you managed to load the project successfully. If you want a quick overview of a topic map, try menu option Layers > Statistics > Topic map info... It will show some additional numbers such as subject identifier and occurrence counts.

If I understand your problem right, you search for [null] in the finder tab and get a search result containing only three topics but expect to get much more topics, right?

You could try the Finder with a dot character (.). It matches any character in regular expressions and the Finder should really list all 53 topics you have in your topic map. You could also try the menu option Edit > Search. It has more powerful search options than the Finder.

Yes, I would be very careful in deleting base ontology topics. Usually it ruins some features of the application. Much better option is to create an empty topic map layer [1] and use it. But still, deleting base ontology topics shouldn't affect the project saving. I have to investigate the problem more detailed, I think.

Kind Regards,
Aki / Wandora Team

[1] http://wandora.org/wiki/Creating_new_layers

Hi Aki,

I tryied to re-create the project without deleting anytine on the Base Layer.
So I created a new Memory Layer and re-created my topics and associations.
But even with this new project, I still have the same import behavior : only few topics are re-imported when I open the project.
The Base Layer is (26,48) and My own Layer is (30,32).

I found 2 strange behaviors:

1/ When I save once again (with diff name) my project I just opened, some topics appears in the "Topics" pannel.

2/ I have the feeling that the topics appears one by one in the Topics panel.
I tryied 3 times to search the dot (.) in the Finder panel :
It founds 11, then 13, then 15 objects !

[Edit] Unfortunately, It stopped at 15 objects. And another try hasn't givent the same behaviour.


[Edit 2] I understood the behaviour :
When I open a topic in a "Traditional" View and the topic contain some Association that I can't see in Topics panel, I can run seach and the hidden objects appears !

[Edit 3] Even by double clicking on the associations in Traditional view, then refresh the Topics panel, new topics appears

Hello Damien

Very strange behavior you have found, I must agree

The Topics tab you see left just above layers views only Wandora class topic and all instances and subclasses of it (by default). You can open topics by clicking the handle left to the topic but your view is always limited to instance and subclass relations (by default). Usually the topic map contains at least some topics that don't appear in Topics tab. You have to locate those topics using other methods. The Finder tab is usually the best choice to find such topics.

The Finder tab, just beside the Topics tab, is used to search topics. The Finder has a text field and the user should write a regular expression into. The Finder views topics that matches given regular expression. And searching with a dot character (.) should find and list all topics in visible topic maps.

If you have two layers and check the number of topics in both layers. If first layer contains 26 topics and second layer 30 topics, it is possible that the overall number of topics is not 56 but lower. This is because some topics may be merged ones i.e. same topic appears in both layers. Wandora obviously finds only one topic for these merged topics. However, the overall number of topics can't be smaller than the (largest) number of a single layer.

If you perform three identical searches and don't change topic map in between, all searches should return same number of topics. Thus, I found very interesting that you managed to find 11, then 13 and finally 15 topics. If you have really not changed any topic nor performed any other operations, you have really spotted a bug in Wandora. I have a hunch that you have managed to create a broken topic that disturbs the Finder. The find operations fails before it finishes. Could you please check the console window if it contains some Java exceptions.

Also, which platform are you using (Linux, PC, Mac) and what is your Java version?

Yes, sometimes the Topics panel doesn't update/redraw and the user has to refresh it. Usually it should update itself automatically after every operation. This may be due to your Java and platform version.

Kind regards,
Aki / Wandora Team

Hi Aki,

Here is my workstation hardware/software configuration

System :

Code: Select all

OS Name: Microsoft Windows 7 Enterprise
OS Version: 6.1.7601 Service Pack 1 Build 7601
OS Manufacturer: Microsoft Corporation
OS Configuration: Member Workstation
OS Build Type: Multiprocessor Free
System Type: x64-based PC


Java :

Code: Select all

>java -version
java version "1.7.0"
Java(TM) SE Runtime Environment (build 1.7.0-b147)
Java HotSpot(TM) 64-Bit Server VM (build 21.0-b17, mixed mode)


Here is the logs for the following scenario with associated logs :
1 / Start Wandora

Code: Select all

*****************************************************
***  WANDORA - KNOWLEDGE MANAGEMENT ENVIRONMENT   ***
***     Copyright (C) 2004-2014 Wandora Team      ***
***              http://wandora.org               ***
*****************************************************
Xms750m Xmx1000m
Changing consistency check to 'false'.
Using XTM 2.0 parser
Importing XTM (2.0) topic map.
Found 26 topics, 48 associations and 12 occurrences.
Restoring consistency check to 'true'.


2 / Loading Project (Only one topic appears)
No logs appears

3 / Double clicking on the topic through the "Topics" pannel : Error 1 :

Code: Select all

Failed to initialize associations!
java.lang.NullPointerException
        at org.wandora.topicmap.layered.LayeredTopic._addAssociations(LayeredTopic.java:929)
        at org.wandora.topicmap.layered.LayeredTopic.getAssociations(LayeredTopic.java:969)
        at org.wandora.application.gui.topicpanels.AbstractTopicPanel.buildAssociationsPanel(AbstractTopicPanel.java:184)
        at org.wandora.application.gui.topicpanels.TraditionalTopicPanel.refresh(TraditionalTopicPanel.java:399)
        at org.wandora.application.gui.topicpanels.TraditionalTopicPanel.open(TraditionalTopicPanel.java:148)
        at org.wandora.application.gui.topicpanels.DockingFramePanel.addDockable(DockingFramePanel.java:492)
        at org.wandora.application.gui.topicpanels.DockingFramePanel.open(DockingFramePanel.java:187)
        at org.wandora.application.gui.topicpanels.TopicPanelManager.openTopic(TopicPanelManager.java:440)
        at org.wandora.application.Wandora.openTopic(Wandora.java:1456)
        at org.wandora.application.Wandora.applyChangesAndOpen(Wandora.java:1492)
        at org.wandora.application.gui.tree.TopicTree.mouseClicked(TopicTree.java:642)
        at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
        at java.awt.Component.processMouseEvent(Unknown Source)
        at javax.swing.JComponent.processMouseEvent(Unknown Source)
        at java.awt.Component.processEvent(Unknown Source)
        at java.awt.Container.processEvent(Unknown Source)
        at java.awt.Component.dispatchEventImpl(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
        at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
        at java.awt.Container.dispatchEventImpl(Unknown Source)
        at java.awt.Window.dispatchEventImpl(Unknown Source)
        at java.awt.Component.dispatchEvent(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$000(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue$4.run(Unknown Source)
        at java.awt.EventQueue$4.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)


4 / Doing "Refresh tree" on the Topics pannel :
=> Some new topics appears in the pannel + Error 2 :

Code: Select all

java.lang.NullPointerException
        at org.wandora.topicmap.layered.LayeredTopic._addAssociations(LayeredTopic.java:929)
        at org.wandora.topicmap.layered.LayeredTopic.getAssociations(LayeredTopic.java:969)
        at org.wandora.application.gui.topicpanels.AbstractTopicPanel.buildAssociationsPanel(AbstractTopicPanel.java:184)
        at org.wandora.application.gui.topicpanels.TraditionalTopicPanel.refresh(TraditionalTopicPanel.java:399)
        at org.wandora.application.gui.topicpanels.DockingFramePanel.refresh(DockingFramePanel.java:231)
        at org.wandora.application.gui.topicpanels.DockingFramePanel.doRefresh(DockingFramePanel.java:668)
        at org.wandora.application.Wandora.doRefresh(Wandora.java:341)
        at org.wandora.application.tools.AbstractWandoraTool$1.run(AbstractWandoraTool.java:245)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$000(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)


Hope it helps
Regards,
Damien.

Hi Damien

Thank you very much for the information. Looking at the Java exceptions in your post, it really looks like we have a problem in Wandora.

I wonder if the Wandora project file that triggers these problems contains any sensitive information? Do you think you could send it to me for more detailed inspection? If this is ok to you, please, send the project file to email address support (at) wandora.org .

Kind Regards,
Aki / Wandora Team

Hello Aki,

OK files sent with my professional email address.

Best regards.

Hello Aki,

Did you reproduce the problem with the project I sent to you ?

Regards.
Damien.

Hello Damien

Ok, I found the problem. Wandora uses temporary subject identifiers while importing a project file. After the project has been loaded, Wandora removes these temporary subject identifiers. Unfortunately Wandora also removed actual subject identifiers that only resemble temporary subject identifiers i.e. start with http://wandora.org/si/temp.... After the removal, topics have no subject identifiers at all and Wandora doesn't work properly but fails in many ways.

I have updated Wandora's distribution packages with a fixed version at

http://www.wandora.org/download/wandora.zip
http://www.wandora.org/download/wandora-src.zip

The bug fix version has a build date 2014-05-13.

Once you have updated Wandora application, you should be able to load and use your project file without problems.

I thank you very much for reporting the problem and the patience in replying my questions. Thank you.

Kind Regards,
Aki / Wandora Team