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Bug #3108

ENM GARP Baseline 3-Actor GARP - Browser Display demo fails with NameDuplication: convertTo?

Added by Christopher Brooks over 11 years ago. Updated about 11 years ago.

Status:
Resolved
Priority:
Normal
Category:
core
Target version:
Start date:
01/28/2008
Due date:
% Done:

0%

Estimated time:
Bugzilla-Id:
3108

Description

The problems below are probably common knowledge, but I've fixed up
the "about:" facility so that it will traverse the demos and try to open
them. This makes it much easier to quickly try these out.

The first Ecological Niche Modeling (GARP) Workflow:
Baseline 3-Actor GARP -Browser Display demo fails.

This is the first Kepler Demo. . .

ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "convertTo" into a container that already contains an object with that name.
at ptolemy.kernel.util.NamedList.append(NamedList.java:125)
at ptolemy.kernel.util.NamedObj._addAttribute(NamedObj.java:2054)
at ptolemy.kernel.util.Attribute.setContainer(Attribute.java:383)
at ptolemy.kernel.util.Attribute.<init>(Attribute.java:109)
at ptolemy.kernel.util.Attribute.<init>(Attribute.java:86)
at ptolemy.kernel.util.AbstractSettableAttribute.<init>(AbstractSettableAttribute.java:88)
at ptolemy.kernel.util.StringAttribute.<init>(StringAttribute.java:110)
at sun.reflect.GeneratedConstructorAccessor1.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
at ptolemy.moml.MoMLParser._createInstance(MoMLParser.java:3985)
at ptolemy.moml.MoMLParser._handlePropertyElement(MoMLParser.java:5068)
at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2784)
at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)
at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)
at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)
at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)
at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)
at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)
at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)
at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)
at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)
at ptolemy.actor.gui.PtolemyEffigy$Factory.createEffigy(PtolemyEffigy.java:412)
at ptolemy.actor.gui.EffigyFactory.createEffigy(EffigyFactory.java:209)
at ptolemy.actor.gui.Configuration.openModel(Configuration.java:595)
at ptolemy.actor.gui.Configuration.openModel(Configuration.java:555)
at ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:264)
at javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)
at javax.swing.text.html.HTMLEditorKit$LinkController.activateLink(HTMLEditorKit.java:827)
at javax.swing.text.html.HTMLEditorKit$LinkController.mouseClicked(HTMLEditorKit.java:637)
at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:212)
at java.awt.Component.processMouseEvent(Component.java:5504)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
at java.awt.Component.processEvent(Component.java:5266)
at java.awt.Container.processEvent(Container.java:1966)
at java.awt.Component.dispatchEventImpl(Component.java:3968)
at java.awt.Container.dispatchEventImpl(Container.java:2024)
at java.awt.Component.dispatchEvent(Component.java:3803)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3901)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
at java.awt.Container.dispatchEventImpl(Container.java:2010)
at java.awt.Window.dispatchEventImpl(Window.java:1778)
at java.awt.Component.dispatchEvent(Component.java:3803)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

The third GARP demo, "3. GARP with Occurrence Data from Digir/Ecogrid"
also fails:
java.io.FileNotFoundException: C:\cxh\src\kepler\workflows\eco\garpModel_ImageJ_withData.xml (The system cannot find the file specified)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:106)
at java.io.FileInputStream.<init>(FileInputStream.java:66)
at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)
at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)
at java.net.URL.openStream(URL.java:1007)

There are plenty of other errors as well.

One quick way to check for missing demos is to use the "about:" feature
in ptolemyII.
To do this:
1. Start Kepler with ant run-dev
2. Help -> Documentation -> Kepler Introduction for Scientists
-> Ptolemy Introduction -> Copyright
3. Select "copyright" in "Other copyrights about this configuration (may take a moment to run)."
4. Select "about" in "Other information about this configuration."
5. Select " Open the .htm, .html, .xml and .pdf " for the introScientist.htm
and introProgrammer.htm files.

It is also possible to check for sizes and centering from the same page.
The sizes are set for XGA (1024x768), which is the size laptop that I have
and Edward may or may not have.

History

#1 Updated by Dan Higgins over 11 years ago

I cannot figure out just what workflows the errors reported correspond to. e.g 'Baseline 3-Actor GARP -Browser Display' doesn't appear to be the name of any workflows.

All the workflows in $KEPLER/demos/ENM work for me when opened individually.

One possibility is opening workflows with EML or DiGir date sources with the PTII about: may not work properly due to use of Kepler caching?

I am moving this to 1.0 release for further investigation.

Dan Higgins

#2 Updated by Christopher Brooks over 11 years ago

To replicate this,
1. ant run-dev
2. In the Welcome Window, click on "Getting Started"
3. This brings up kepler/configs/ptolemy/configs/kepler/introScientists.htm
4. Click on "ENM (GARP) Workflows
5. This brings up kepler/configs/ptolemy/configs/kepler/ENM_Workflows.html
6. Click on the first link, "1. Baseline 3-Actor GARP - Browser Display"
The corresponding link is kepler/workflows/eco/garpModel.xml
I get:

ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "convertTo" into a container that already contains an object with that name.

#3 Updated by Chad Berkley over 11 years ago

We should not be linking to any workflows that do not work. All html links need to be checked and if any broken workflow links are found, they should be removed.

#4 Updated by Sean Riddle about 11 years ago

A workflow in the workflows/ folder doesn't affect Kepler 1.0, since we're not releasing it, just demos/

#5 Updated by Redmine Admin over 6 years ago

Original Bugzilla ID was 3108

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