problems parsing xml with dtd from a foreign source

[Donald Ball]

(sent to cocoon-users, no help there...)

hey guys. i'm trying to retrieve some xml content over http to begin one
of my pipelines:

/nlm/query?author=Smith

<map:match pattern="nlm/query">
  <map:match type="request" pattern="author">
    <map:generate 
src="http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi?db=PubMed&amp;mode=XML&amp;dispmax=999&amp;term={1}[au]"/>
    <map:serialize type="xml"/>
  </map:match>
</map:match>

the xml returned from the nih server will begin like so:

<?xml version="1.0"?>
<!DOCTYPE QueryResult PUBLIC "-//NLM//DTD QueryResult, 22 Jan 2002//EN"
"/entrez/query/DTD/pmqty_020122.dtd" >
<QueryResult>

unfortunately, i get an exception when cocoon tries to parse this
document. it claims that it cannot access the dtd:

java.net.MalformedURLException: no protocol:
/entrez/query/DTD/pmqty_020122.dtd
        at java.net.URL.(URL.java:473)
        at java.net.URL.(URL.java:376)
        at java.net.URL.(URL.java:330)
        at
org.apache.xerces.impl.XMLEntityManager.startEntity(XMLEntityManager.java:731)
        at
org.apache.xerces.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:691)
        at
org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:258)
        at
org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(XMLDocumentScannerImpl.java:811)
        at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:333)
        at
org.apache.xerces.parsers.StandardParserConfiguration.parse(StandardParserConfiguration.java:525)
        at
org.apache.xerces.parsers.StandardParserConfiguration.parse(StandardParserConfiguration.java:581)
        at org.apache.xerces.parsers.XMLParser.parse(XMLParser.java:147)
        at
org.apache.xerces.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1157)
        at
org.apache.avalon.excalibur.xml.JaxpParser.parse(JaxpParser.java:241)
        at
org.apache.cocoon.components.source.AbstractStreamSource.toSAX(AbstractStreamSource.java:204)
        at
org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:142)

shouldn't it be trying to download the DTD from this url:

http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pmqty_020122.dtd

where it does, in fact, live?

i did manage to work around this problem using the excellent entity
catalogs facility, and i suspect that's what we'll want to use in the long
term, but i would like to track down why this isn't working as (i think)
it ought to. thanks in advance.

- donald


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