Weird (well for me anyway) SAX parsing problem

Hi,
I have to use SAX to parse huge XML files (the biggest is around 8Gb; genomic data) and input into MySQL. I get an IndexOutOfBoundException when I try to parse a perfectly valid string of an element after a few thousands entries.
Let's say that my string is "G/T". I use split("/") to get the string array and get item[0] and item[1]. The error comes up always when I try to read item[1]. What is the weird part is that if I take out the already read part of the file, it is read perfectly up until a few thousand elements againn with the same error.
Any insights would be gladly appreciated
Sylvain Foisy, Ph. D.
Bio-informatician
Inflammgen.org
Montreal Cardiology Institute
Montreal,Qc

Hi,
In the characters() method from DefaultHandler, it seems that every once in a while the string returned is not read in full by the parser. The string returned for this element can only be someting like "G/T". When the parser breaks, I get that "G/" string instead. The logic of the parser goes like this:
-look for tag OBSERVED;
-when found, get the string attached to it (something like "G/T");
-split in two chars: G and T
-assigned the chars to variables.
I know that the problem comes from the parser not getting the whole string, just part of it therefore my IndexOutOfBoundException.
I am looking for a way to for the parser to get the whole string.
A+
Sylvain Foisy, Ph. D.
Bio-informatician
Inflammgen.org
Montreal Cardiology Institute
Montreal,Qc

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What I expect the problem to be was discussed recently in a topic titled "SAX Parser Problems" that was started on March 14 at 6:59 AM by JackoBS.
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import java.io.*;
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pp_transid = strsplit(Opp_transid);
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pp_respmsg = strsplit(Opp_respmsg);
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pp_authid = strsplit(Opp_authid);
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java.util.NoSuchElementException
at org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:691)
at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
at org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:345)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:281)
at Echo03.main(Echo03.java:47)

I haven't gone through your code but I also had a similar error....and the exception in my was because of an "&" instead of the entity reference & in one of the element values. I use a non-validating parser but if you use a validating one then this might not be the reason for your exception.

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Thanks for reading this msg!
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XML element :
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This is a FAQ, search the forums or look at the API documentation
http://java.sun.com/j2se/1.4.2/docs/api/org/xml/sax/ContentHandler.html#characters(char[],%20int,%20int)
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2. Due to performance issues we parse the input stream from the CLOB.
3. For same reason, we are not using XSL.
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We already tried that..looks like the line where I mentioned that it converted the entity referece characters to an ampersand..
"We tried using <entity reference for &> but it then breaks it up into SomeText_A, & and SomeText_B."
null

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I’m having problems getting an xml document to validate within Weblogic 8.1. I am trying to parse a document that references both a dtd and xsd. Both the schema and dtd reference need to be substituted so they use local paths. I specify the schema the parser should use and have created an entityResolver to change the dtd reference.
When this runs as a standalone app from eclipse the file parses and validates without a problem. When deployed to the app server the process seems to be unable read the contents of the dtd. Its not that it cannot find the file (no FileNotFoundException is thrown but this can be created if I delete the dtd) rather it seems to find no declared elements.
Initial thought was that the code didn’t have access to read the dtd from its location on disk, to check I moved the dtd to within the deployed war and reference as a resource. The problem still persists.
Code Snippet:
boolean isValid = false;
try {
     // Create and configure factory
SAXParserFactory factory = SAXParserFactoryImpl.newInstance();
factory.setValidating(true);
factory.setNamespaceAware(true);
// To be notified of validation errors in the XML document,
// add a custom error handler to the document builder
PIMSFeedFileValidationHandler handler
= new PIMSFeedFileValidationHandler();
     // Create and Configure Parser
SAXParser parser = factory.newSAXParser();
parser.setProperty(JAXP_SCHEMA_LANGUAGE, W3C_XML_SCHEMA);
parser.setProperty(NAMESPACE_PROPERTY_KEY, getSchemaFilePath());
     // Set reader with entityResolver for dtd
XMLReader xmlReader = parser.getXMLReader();
xmlReader.setEntityResolver(new SAXEntityResolver(this.dtdPath));
// convert file to URL, as it is a remote file
URL url = super.getFile().toURL();
// Open an input stream and parse
InputStream is = url.openStream();
xmlReader.setErrorHandler(handler);
xmlReader.parse(new InputSource(is));
is.close();
// get the result of parsing the document by checking the
// errorhandler's isValid property
isValid = handler.isValid();
if (!isValid) {
LOGGER.warn(handler.getMessage());
LOGGER.debug("XML file is valid XML? " + isValid);
} catch (ParserConfigurationException e) {
LOGGER.error("Error parsing file", e);
} catch (SAXException e) {
LOGGER.error("Error parsing file", e);
} catch (IOException e) {
throw new FeedException(e);
return isValid;
See stack trace below for a little more info.
2005-01-28 10:24:09,217 [DEBUG] [file] - Attempting validation of file 'cw501205.wa1.xml' with schema at 'C:/pims-feeds/hansard/schema/hansard-v1-9.xsd'
2005-01-28 10:24:09,217 [DEBUG] [file] - Entity Resolver is using DTD path file:C:/Vignette/runtime_services/8.1/install/common/nodemanager/
VgnVCMServer/stage/pims-hansard/pims-hansard.war/WEB-INF/classes/com/morse/pims/cms/feed/sax/ISO-Entities.dtd
2005-01-28 10:24:09,227 [DEBUG] [file] - Creating InputSource at: file:C:/Vignette/runtime_services/8.1/install/common/nodemanager/VgnVCMServer/stage/pims-hansard/pims-hansard.war/WEB-INF/classes/com/morse/pims/cms/feed/sax/ISO-Entities.dtd
2005-01-28 10:24:09,718 [WARN ] [file] - org.xml.sax.SAXParseException: Element type "Hansard" must be declared.
org.xml.sax.SAXParseException: Element type "Session" must be declared.
org.xml.sax.SAXParseException: Element type "DailyRecord" must be declared.
org.xml.sax.SAXParseException: Element type "Volume" must be declared.
org.xml.sax.SAXParseException: Element type "Written" must be declared.
org.xml.sax.SAXParseException: Element type "WrittenHeading" must be declared.
org.xml.sax.SAXParseException: Element type "Introduction" must be declared.
… continues for all the elements in the doc
2005-01-28 10:24:10,519 [DEBUG] [file] - XML file is valid XML? false
2005-01-28 10:24:10,519 [WARN ] [file] - Daily Part file 'cw501205.wa1.xml' was not valid XML and was not processed.
Has anybody seen this behavior before with weblogic and if so how have you resolved the issue.
Thanks in Advance
Adam

Hi David,
I have checked the ejb-jar.xml file and there is no duplicate values in it and the other things is that the same application is been deployed on OAS 10G and websphere and its working fine. In the forum someone has replied to a similar problem that there is bug in Weblogic 10.3 and its CR no 376292. I am not sure about it, does anyone any information about it.
Thanks and Regards
Deepak Dani

Weird (well for me anyway) SAX parsing problem

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