In trying to get Pub2TEI working on the grobid gold standard data from PMC, I ran into the DTD issues mentioned in the README. After some research, I was able to discover that DTD loading can be disabled with the following switch:

--parserFeature?uri=http%3A//apache.org/xml/features/nonvalidating/load-external-dtd:false

References:

• Saxon docs on the --feature switch
• StackOverflow response from Saxon developer Michael Kay
• Xerces Documentation on load-external-dtd

I've attached a file from the grobid PMC gold standard data I was having trouble with. The new switch allows the conversion to proceed.

sample.zip

The sample command in the README could be updated to:

java -jar Samples/saxon9he.jar \
	--parserFeature?uri=http%3A//apache.org/xml/features/nonvalidating/load-external-dtd:false \
	-a:off \
	-dtd:off \
	-expand:off \
	-o:out.tei.xml \
	-s:Samples/TestPubInput/BMJ/bmj_sample.xml \
	-t \
	-xsl:Stylesheets/Publishers.xsl