Bugs item #1117801, was opened at 2005-02-07 05:06
Message generated for change (Comment added) made by gaaschk26
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Peter Murray-Rust (petermr)
Assigned to: Nobody/Anonymous (nobody)
Summary: CML namespace failure with Java1.5
Initial Comment:
The following "CML" file from our Xindice database
<entry src:col="/db/wwmm/nci/entry"
src:key="nci_006229.xml">
<identifier tautomeric="0" version="0.932Beta">
<basic>C10H8,1H-2H-6H-10-8H-4H-3H-7H-9(10)5H-
1</basic>
<charge/>
</identifier>
<molecule formalCharge="0" id="NSC6229">
<formula>C 10 H 8</formula>
<metadata>
<module role="init">
<module role="header">
<list>
<scalar dictRef="ccml:program">MOPAC2002
(c) Fujitsu</scalar>
<scalar dictRef="ccml:method">PM5</scalar>
<scalar
dictRef="ccml:program">MOPAC2002</scalar>
...
</entry>
has namespaced prefixes added by Xindice but without
the namespace URI (xmlns:src). This is an invalid file if
validation is enforced but I think is otherwise OK. Under
java1.4 there is no problem but under 1.5 the applet
stops at a black background with the Java console error:
SmarterJmolAdapter:The Resolver thinks:Cml
SmarterJmolAdapter:The Resolver thinks:Cml
SmarterJmolAdapter:The Resolver thinks:Cml
SmarterJmolAdapter:The Resolver thinks:Cml Using
JAXP/SAX XML parser. Using JAXP/SAX XML parser.
Using JAXP/SAX XML parser. SAX FATAL:The prefix "src"
for attribute "src:col" associated with an element
type "molecule" is not bound.
org.xml.sax.SAXParseException: The prefix "src" for
attribute "src:col" associated with an element
type "molecule" is not bound.
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAX
Parser.parse(Unknown Source)
at
org.jmol.adapter.smarter.CmlReader.readAtomSetCollect
ion(CmlReader.java:71)
at org.jmol.adapter.smarter.Resolver.resolve
(Resolver.java:57)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.openBuffe
redReader(SmarterJmolAdapter.java:62) SAX
FATAL:The prefix "src" for attribute "src:col" associated
with an element type "entry" is not bound.
at
org.jmol.viewer.FileManager$FileOpenThread.openReade
r(FileManager.java:435)
at org.jmol.viewer.FileManager$FileOpenThread.run
(FileManager.java:397)
at org.jmol.viewer.FileManager.openStringInline
(FileManager.java:105)
at org.jmol.viewer.Viewer.openStringInline
(Viewer.java:966)
at org.jmol.applet.JmolApplet.loadInline
(JmolApplet.java:454)
at org.jmol.applet.JmolApplet.initApplication
(JmolApplet.java:248)
at org.jmol.applet.JmolApplet.init
(JmolApplet.java:125)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source) error
opening string org.xml.sax.SAXParseException: The
prefix "src" for attribute "src:col" associated with an
element type "molecule" is not bound.
org.xml.sax.SAXParseException: The prefix "src" for
attribute "src:col" associated with an element
type "entry" is not bound.
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAX
Parser.parse(Unknown Source)
at
org.jmol.adapter.smarter.CmlReader.readAtomSetCollect
ion(CmlReader.java:71)
at org.jmol.adapter.smarter.Resolver.resolve
(Resolver.java:57)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.openBuffe
redReader(SmarterJmolAdapter.java:62)
at
org.jmol.viewer.FileManager$FileOpenThread.openReade
r(FileManager.java:435)
at org.jmol.viewer.FileManager$FileOpenThread.run
(FileManager.java:397)
at org.jmol.viewer.FileManager.openStringInline
(FileManager.java:105)
at org.jmol.viewer.Viewer.openStringInline
(Viewer.java:966)
at org.jmol.applet.JmolApplet.loadInline
(JmolApplet.java:454)
at org.jmol.applet.JmolApplet.initApplication
(JmolApplet.java:248)
at org.jmol.applet.JmolApplet.init
(JmolApplet.java:125)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source) error
opening string org.xml.sax.SAXParseException: The
prefix "src" for attribute "src:col" associated with an
element type "entry" is not bound. Using JAXP/SAX XML
parser. SAX FATAL:The prefix "src" for
attribute "src:col" associated with an element
type "molecule" is not bound.
org.xml.sax.SAXParseException: The prefix "src" for
attribute "src:col" associated with an element
type "molecule" is not bound.
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAX
Parser.parse(Unknown Source)
at
org.jmol.adapter.smarter.CmlReader.readAtomSetCollect
ion(CmlReader.java:71)
at org.jmol.adapter.smarter.Resolver.resolve
(Resolver.java:57)
at
org.jmol.adapter.smarter.SmarterJmolAdapter.openBuffe
redReader(SmarterJmolAdapter.java:62)
at
org.jmol.viewer.FileManager$FileOpenThread.openReade
r(FileManager.java:435)
at org.jmol.viewer.FileManager$FileOpenThread.run
(FileManager.java:397)
at org.jmol.viewer.FileManager.openStringInline
(FileManager.java:105)
at org.jmol.viewer.Viewer.openStringInline
(Viewer.java:966)
at org.jmol.applet.JmolApplet.loadInline
(JmolApplet.java:454)
at org.jmol.applet.JmolApplet.initApplication
(JmolApplet.java:248)
at org.jmol.applet.JmolApplet.init
(JmolApplet.java:125)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
error opening string
...... and more
I think this should be trapped and reported as it fooled
us for at least a day! In the future it is almost certain
that people will submit invalid files on a regular basis
and so validation should be switched off by default.
----------------------------------------------------------------------
Comment By: Kevin Gaasch (gaaschk26)
Date: 2005-07-10 18:09
Message:
Logged In: YES
user_id=1308816
Could you attach a copy of the file? I would like to run
some tests and see if I can duplicate the error.
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