Bug 657 – Jython import of ETree fails on the second run of a script, but not in Jython interpreter

Bug 657 - Jython import of ETree fails on the second run of a script, but not in Jython interpreter


Summary:	Jython import of ETree fails on the second run of a script, but not in Jython...

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2013-08-30 04:34 CDT by Jean-Yves Tinevez
Modified:	2013-09-05 10:55 CDT
CC List:	3 users (show)

See Also:

Description Jean-Yves Tinevez 2013-08-30 04:34:50 CDT

Hi all, 
I have this bug that seems to be a big in the Script Editor import mechanism. 

I am writing a script that involves reading xml, for which I use ElementTree. 
In the script editor, a script will run *only once* On the second run, it will generate an error I copy below.

For instance, try to run this simple Jython script:

import xml.etree.ElementTree
xmlfile = '/Users/tinevez/Desktop/ExampleXMLFile.xml'
tree = xml.etree.ElementTree.parse(xmlfile) 
print(tree)

The first time it will run and show:
<xml.etree.ElementTree.ElementTree instance at 0x9>


The second time it will generate the following error:
Started FailJythonImport.py at Fri Aug 30 11:33:32 CEST 2013
Traceback (most recent call last):
  File "<iostream>", line 4, in <module>
  File "/Users/tinevez/Applications/Fiji/Fiji.app/jars/jython.jar/Lib/xml/etree/ElementTree.py", line 862, in parse
  File "/Users/tinevez/Applications/Fiji/Fiji.app/jars/jython.jar/Lib/xml/etree/ElementTree.py", line 581, in parse
  File "/Users/tinevez/Applications/Fiji/Fiji.app/jars/jython.jar/Lib/xml/etree/ElementTree.py", line 1120, in __init__
  File "/Users/tinevez/Applications/Fiji/Fiji.app/jars/jython.jar/Lib/xml/parsers/expat.py", line 63, in ParserCreate
  File "/Users/tinevez/Applications/Fiji/Fiji.app/jars/jython.jar/Lib/xml/parsers/expat.py", line 91, in __init__
	at org.xml.sax.helpers.XMLReaderFactory.loadClass(XMLReaderFactory.java:205)
	at org.xml.sax.helpers.XMLReaderFactory.createXMLReader(XMLReaderFactory.java:196)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
org.xml.sax.SAXException: java.lang.ClassNotFoundException: org.python.apache.xerces.parsers.SAXParser


This does not happen if the script is copied in the Jython Interpreter, even several times

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.7.5
  java.version => 1.6.0_51
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_51-b11-457-11M4509
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.51-b01-457
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Users/tinevez/Applications/Fiji/Fiji.app

Information about the version of each plugin:

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  7e27d804 20130624163910 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  16012d5a 20130624163910 plugins/registration_3d-2.0.0-SNAPSHOT.jar
  e6e0879f 20110303204101 retro/backport-util-concurrent-3.1.jar
  8759ba20 20130417153743 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 20130417153745 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 20120510154415 scripts/InstallJava3D.m
  05a92a3c 20120510154415 scripts/IsJava3DInstalled.m
  ff34d026 20120809095414 scripts/Matlab3DViewerDemo_1.m
  25be149f 20120510154415 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20120809095414 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20120809095414 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20120809095414 scripts/Miji.m
  868cd434 20120510154412 scripts/Miji_Test.m
  dc94c3a3 20120510154412 scripts/bfopen.m
  a77cab39 20130808170630 scripts/importTrackMateTracks.m

Comment 1 Johannes Schindelin 2013-09-04 13:56:08 CDT

Thanks for the report! I fixed this in https://github.com/fiji/fiji/commit/9b4e4f1071357aea8df09e21404ee7a916f1083c and uploaded it.

Comment 2 Jean-Yves Tinevez 2013-09-05 10:55:47 CDT

Thanks Johannes, it works like a charm.