Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

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Hi Rutger,

Thanks for spending all this time working through this!

When I've used the url https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java for checkout, rather than https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ I don't have the Examples folder that the hyperlink.xml file is in, so I can't read that.

But about using the first url, I now have the problem that when I try to export in Nexml I no longer get the default hyperlink.xml that treated hyperlink as a predicate; instead it crashes, with the log file reproduced below. What's odd is that for Mesquite to even load nexml now, predicateHandlerMapping.properties must be commented out. 

So, two log files. The fist is where the .properties file is commented out in my classpaths.xml file and thus Mesquite loads the nexml module, provides exporting as NeXml as an option, but crashes when I try to export. The second is when the .properties file isn't commented out in my classpaths.xml file, but not you don't see that Mesquite loads nexml in the log.

Error message when I try to export with nexml. Log:

Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/dom4j-1.6.1.jar
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/JSci.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/pal.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/Jama-1.0.1.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/iText.jar
Mesquite version 2.6+ (build 499)
Copyright (c) 1997-2009 W. Maddison and D. Maddison
The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License.   Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.  For details on license and lack of warranty see the GNU Lesser General Public License by selecting "Display License" from the Window menu or at www.gnu.org

Principal Authors: Wayne Maddison & David Maddison
Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver
Development Team Alumnus: Danny Mandel

Wed Jun 10 16:25:01 EDT 2009
Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on Linux 2.6.28-13-generic (architecture: i386)
User: kasia

Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/  dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar

Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/
Log file located in: /home/kasia/Mesquite_Support_Files
Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs

Modules loading from directory /home/kasia/workspace/Mesquite Project/Mesquite_Folder/mesquite/

 ancstates basic categ charMatrices charts cont genesis io lists minimal parsimony stochchar trees align assoc batchArch coalesce consensus correl distance diverse dmanager mb meristic molec ornamental pairwise rhetenor search tol treefarm iText jama jsci pal trunk

Additional modules loaded from /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder

Additional modules loaded from /home/kasia/workspace/nexmltest/java/bin
 nexml

687 modules installed.
1 prerelease substantive modules installed.

Mesquite makes use of BrowserLauncher by Eric Albert,  corejava.Format by Horstmann & Cornell, and iText by Lowagie & Soares

------------------------------

THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this version without permission of authors.

Loading manual for searching..... manual ready.
Mesquite > openGeneral "Open_URL"
Opening external
     at Wed Jun 10 16:25:13 EDT 2009
Dialog box shown.  Title: Open URL

For console choice use component numbers
     1 <blank>
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a editable text, enter
 both number of component and the text within it
 (e.g. if you want to specify the text for component 1 to be "100.0",
 enter "1 100.0"

(Open URL) # 
(Mesquite) # Dialog closed
Location: http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex

Reading NEXUS file hyperlink.nex
Reading block: TAXA
Reading block: TREES
Reading block: NOTES
Reading block: MESQUITE
File reading complete (file hyperlink.nex)
Basic File Coordinator > export
Dialog box shown.  Title: Export format

For console choice use component numbers
      Export part or all of the information as a file of the following format
     --------------
     1 List 
       1 *Export NEXUS Tree File
       2  Export NEXUS Tree File from Tree Source
       3  Phylip (trees)
       4  Export Taxa Distance Matrix
       5  NeXML (taxa, matrices, trees and annotations)
     --------------
      Exports NEXUS file with a tree block, and optionally a taxa block.
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a list or choice menu, enter
 both number of component and number of item within it to choose
 (e.g. if a list is component 1, and you want to select its item 2, enter "1 2"

(Export format) # 
(Mesquite) # Dialog closed
(Following stack trace from object of class: class mesquite.lib.PendingCommand)
java.lang.NullPointerException
	at java.util.Properties$LineReader.readLine(Properties.java:418)
	at java.util.Properties.load0(Properties.java:337)
	at java.util.Properties.load(Properties.java:325)
	at mesquite.nexml.InterpretNEXML.InterpretNEXML.exportFile(Unknown Source)
	at mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.export(BasicFileCoordinator.java:1003)
	at mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.doCommand(BasicFileCoordinator.java:1488)
	at mesquite.lib.PendingCommand.go(PendingCommand.java:205)
	at mesquite.lib.MainThread.run(MainThread.java:116)

Dialog box shown.  Title: Crash

For console choice use component numbers
      A command could not be completed because an exception occurred (i.e. a crash; class java.lang.NullPointerException ). WARNING: there is a chance this crash could have corrupted your data.  Please check your data carefully.  If you save any files, you might best use Save As... in case file saving doesn't work properly.

Please send a report of this crash to the Mesquite server, to help us debug it and improve Mesquite.  None of your data will be sent, but your log file up to this point will be sent.
     1 (Close without sending)
     2 (OK, Send and Force Quit)
     3 (OK, Send Report and Continue)
Enter number of component to select.

(Crash) # 
(Mesquite) # Dialog closed

- Curiously, when I change my classpaths.xml file so that predicateHandlerMapping isn't commented out, the nexml module doesn't even load and exporting as NeXml isn't an option. classpaths.xml:

<?xml version="1.0"?>
<mesquite>
	<classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
	<classpath>predicateHandlerMapping.properties</classpath>
	<!-- classpath>../../nexml/java</classpath-->
	<!--classpath>../..nexml/java/src</classpath-->

	<!--classpath>../../teest/java/bin</classpath> < The test that worked to bring up nexml option again, but crashed. Only needed this classpath. -->
	<!--classpath>../../nexmltest3/nexml/java/bin</classpath-->
	<classpath>../../nexmltest/java/bin</classpath>

</mesquite>

Log:

Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/dom4j-1.6.1.jar
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/JSci.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/pal.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/Jama-1.0.1.zip
Jar file added to classpath: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/jars/iText.jar
Mesquite version 2.6+ (build 499)
Copyright (c) 1997-2009 W. Maddison and D. Maddison
The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License.   Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.  For details on license and lack of warranty see the GNU Lesser General Public License by selecting "Display License" from the Window menu or at www.gnu.org

Principal Authors: Wayne Maddison & David Maddison
Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver
Development Team Alumnus: Danny Mandel

Wed Jun 10 16:30:03 EDT 2009
Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on Linux 2.6.28-13-generic (architecture: i386)
User: kasia

Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/  dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar

Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/
Log file located in: /home/kasia/Mesquite_Support_Files
Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs

Modules loading from directory /home/kasia/workspace/Mesquite Project/Mesquite_Folder/mesquite/

 ancstates basic categ charMatrices charts cont genesis io lists minimal parsimony stochchar trees align assoc batchArch coalesce consensus correl distance diverse dmanager mb meristic molec ornamental pairwise rhetenor search tol treefarm iText jama jsci pal trunk

Additional modules loaded from /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder

Additional modules loaded from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/predicateHandlerMapping.properties

686 modules installed.
1 prerelease substantive modules installed.

Mesquite makes use of BrowserLauncher by Eric Albert,  corejava.Format by Horstmann & Cornell, and iText by Lowagie & Soares

---------------------

THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this version without permission of authors.

Loading manual for searching..... manual ready.
Mesquite > openGeneral "Open_URL"
Opening external
     at Wed Jun 10 16:31:08 EDT 2009
Dialog box shown.  Title: Open URL

For console choice use component numbers
     1 <blank>
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a editable text, enter
 both number of component and the text within it
 (e.g. if you want to specify the text for component 1 to be "100.0",
 enter "1 100.0"

(Open URL) # 
(Mesquite) # Dialog closed
Mesquite > openGeneral "Open_URL"
Opening external
     at Wed Jun 10 16:31:25 EDT 2009
Dialog box shown.  Title: Open URL

For console choice use component numbers
     1 <blank>
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a editable text, enter
 both number of component and the text within it
 (e.g. if you want to specify the text for component 1 to be "100.0",
 enter "1 100.0"

(Open URL) # 
(Mesquite) # Dialog closed
Location: http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex

Reading NEXUS file hyperlink.nex
Reading block: TAXA
Reading block: TREES
Reading block: NOTES
Reading block: MESQUITE
File reading complete (file hyperlink.nex)
Basic File Coordinator > export
Dialog box shown.  Title: Export format

For console choice use component numbers
      Export part or all of the information as a file of the following format
     --------------
     1 List 
       1 *Export NEXUS Tree File
       2  Export NEXUS Tree File from Tree Source
       3  Phylip (trees)
       4  Export Taxa Distance Matrix
     --------------
      Exports NEXUS file with a tree block, and optionally a taxa block.
     2 (Cancel)
     3 (OK)
Enter number of component to select.
 If component is a list or choice menu, enter
 both number of component and number of item within it to choose
 (e.g. if a list is component 1, and you want to select its item 2, enter "1 2"

(Export format) # 
(Mesquite) # Dialog closed

Kasia

Katherine "Kasia" Hayden
Bennington College, Class of 2011
312.576.8175
kh...@be...

-----Original Message-----
From: Rutger Vos [mailto:rut...@gm...]
Sent: Wed 6/10/2009 3:52 PM
To: Hayden, Katherine M.
Cc: Wayne Maddison; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go...
Subject: Re: [Nexml-discuss] CDAO term inclusion community process

Ok, so now that you have nexml as an export option, could you send the
log for when you're reading the hyperlink.xml file?

On Wed, Jun 10, 2009 at 8:41 AM, Hayden, Katherine
M.<KH...@be...> wrote:
> Hi Rutger,
>
> I couldn't get NeXml as an export option with these new instructions, but
> when I made a test directory and used the old checkout url
> (https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java) the
> option to export as NeXml was back. Still trying to figure out the
> difference.
>
> Kasia
>
>
>
> Katherine "Kasia" Hayden
> Bennington College, Class of 2011
> 312.576.8175
> kh...@be...
>
>
>
> -----Original Message-----
> From: Rutger Vos [mailto:rut...@gm...]
> Sent: Wed 6/10/2009 7:07 AM
> To: Wayne Maddison
> Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli;
> ju...@ig...; nex...@li...;
> ph...@go...
> Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>
> Hi,
>
> Wayne, thanks for chiming in - I changed the way the properties file
> is loaded a little bit (sorry I left the absolute paths in
> previously!). Kasia, could you try the following,
>
> - assuming $NEXMLTRUNK is your local equivalent for
> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
> - assuming $MESQUITE_FOLDER is your local equivalent for
> http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/
>
> * cd $NEXMLTRUNK/java
> * export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
> * ant mesquite
> * pico "$MESQUITE_FOLDER/classpaths.xml"
> * add an entry in classpaths.xml:
> <classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
> be substituted for the real path (either relative or absolute) to the
> bin folder in which ant placed the compiled classes. Attached is how I
> have it, which works when you check the mesquite trunk and the full
> nexml code (trunk and branches) in the same folder (for me that's
> ~/Documents/workspace but it shouldn't matter)
>
> Now, when Mesquite starts up, could you copy and paste what happens in
> the log window when you read the local version of this file:
> $NEXMLTRUNK/examples/translations/hyperlink.xml
>
> Hope this helps!
>
> Rutger