TrakEM concatenate .XML files error

[Ashwin]

Hi all,

I am trying to concatenate two .XML project files using a script provided by Albert (http://fiji.sc/wiki/index.php/TrakEM2_Scripting#Concatenating_multiple_project_XML_files_by_copying_all_their_layers)

I am however running into some errors that I am unable to understand. Once, I run the script, it creates a new project with said name but following that it spits out an error.

Fatal error: column=61 line=269
==================
ERROR:
org.xml.sax.SAXParseException: Element type "project" must be followed by either attribute specifications, ">" or "/>".
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1231)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        at ini.trakem2.persistence.FSLoader.openFSProject(FSLoader.java:291)
        at ini.trakem2.Project.openFSProject(Project.java:554)
        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)
        at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:175)
        at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190)
        at org.python.core.PyObject.__call__(PyObject.java:414)
        at org.python.core.PyObject.__call__(PyObject.java:418)
        at org.python.pycode._pyx10.merge_layers$1(<iostream>:50)
        at org.python.pycode._pyx10.call_function(<iostream>)
        at org.python.core.PyTableCode.call(PyTableCode.java:165)
        at org.python.core.PyBaseCode.call(PyBaseCode.java:117)
        at org.python.core.PyFunction.__call__(PyFunction.java:307)
        at org.python.pycode._pyx10.f$0(<iostream>:53)
        at org.python.pycode._pyx10.call_function(<iostream>)
        at org.python.core.PyTableCode.call(PyTableCode.java:165)
        at org.python.core.PyCode.call(PyCode.java:18)
        at org.python.core.Py.runCode(Py.java:1204)
        at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:200)
        at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:195)
        at Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:72)
        at common.RefreshScripts.runScript(RefreshScripts.java:328)
        at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1216)
        at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1776)
==================


I have used this script in the past without any trouble, but am unable to understand what has changed.

Has anyone encountered a similar problem?

Thanks,
Ashwin

[Albert Cardona-2]

Ashwin,

the error says that the XML is malformed. Open the XML file, go to line
269, and stry to find what XML statement is malformed.

Albert


2013/7/12 Ashwin <[hidden email]>

> Hi all,
>
> I am trying to concatenate two .XML project files using a script provided
> by
> Albert
> (
> http://fiji.sc/wiki/index.php/TrakEM2_Scripting#Concatenating_multiple_project_XML_files_by_copying_all_their_layers
> )
>
> I am however running into some errors that I am unable to understand. Once,
> I run the script, it creates a new project with said name but following
> that
> it spits out an error.
>
> Fatal error: column=61 line=269
> ==================
> ERROR:
> org.xml.sax.SAXParseException: Element type "project" must be followed by
> either attribute specifications, ">" or "/>".
>         at
>
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1231)
>         at
>
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
>         at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
>         at
> ini.trakem2.persistence.FSLoader.openFSProject(FSLoader.java:291)
>         at ini.trakem2.Project.openFSProject(Project.java:554)
>         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)
>         at
> org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:175)
>         at
> org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190)
>         at org.python.core.PyObject.__call__(PyObject.java:414)
>         at org.python.core.PyObject.__call__(PyObject.java:418)
>         at org.python.pycode._pyx10.merge_layers$1(<iostream>:50)
>         at org.python.pycode._pyx10.call_function(<iostream>)
>         at org.python.core.PyTableCode.call(PyTableCode.java:165)
>         at org.python.core.PyBaseCode.call(PyBaseCode.java:117)
>         at org.python.core.PyFunction.__call__(PyFunction.java:307)
>         at org.python.pycode._pyx10.f$0(<iostream>:53)
>         at org.python.pycode._pyx10.call_function(<iostream>)
>         at org.python.core.PyTableCode.call(PyTableCode.java:165)
>         at org.python.core.PyCode.call(PyCode.java:18)
>         at org.python.core.Py.runCode(Py.java:1204)
>         at
> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:200)
>         at
> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:195)
>         at
> Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:72)
>         at common.RefreshScripts.runScript(RefreshScripts.java:328)
>         at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1216)
>         at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1776)
> ==================
>
>
> I have used this script in the past without any trouble, but am unable to
> understand what has changed.
>
> Has anyone encountered a similar problem?
>
> Thanks,
> Ashwin
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/TrakEM-concatenate-XML-files-error-tp5003960.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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