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Published 20 hours ago • verified publisher icon ncbi

Does it support articles from PMC ?

Open unoexperto opened this issue 9 years ago • 6 comments

Does it support articles from PMC ? I tested it on article element from this call

http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:4544069

after running xsltproc jats-html.xsl sample.xml >a.html I get HTML with one blob of text from XML with all tags removed.

unoexperto avatar Oct 06 '15 17:10 unoexperto

The JATS Preview Stylesheets were written as a starting point for rendering JATS XML in HTML.

The XML that you are getting from http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:4544069 is an OAI response. It is not a JATS document.

However, it looks like it contains a JATS XML document (or possibly and NLM 3.0 document) between

and

Jeff

From: Ruslan <[email protected]mailto:[email protected]> Reply-To: ncbi/JATSPreviewStylesheets <[email protected]mailto:[email protected]> Date: Tuesday, October 6, 2015 at 1:12 PM To: ncbi/JATSPreviewStylesheets <[email protected]mailto:[email protected]> Subject: [JATSPreviewStylesheets] Does it support articles from PMC ? (#11)

Does it support articles from PMC ? I tested it on article element from this call

http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:4544069

after running xsltproc jats-html.xsl sample.xml >a.html I get HTML with one blob of text from XML with all tags removed.

— Reply to this email directly or view it on GitHubhttps://github.com/ncbi/JATSPreviewStylesheets/issues/11.

jeffbeckncbi avatar Oct 06 '15 17:10 jeffbeckncbi

Thank you, Jeff. As I mentioned in my original message it I tested it with article element, not with XML returned by API.

unoexperto avatar Oct 06 '15 18:10 unoexperto

Looks like our OAI service is adding a default namespace on the article content, of xmlns="http://dtd.nlm.nih.gov/2.0/xsd/archivearticle. That's a bug in our service. If you strip that out, you'll get better HTML. I'll report this bug.

Klortho avatar Oct 06 '15 18:10 Klortho

That helped! Awesome! Resulting HTML doesn't have correct IMG tags but I'll go through documentation more. Thanks!

unoexperto avatar Oct 06 '15 18:10 unoexperto

Have you guys had a chance to fix this bug ? I still see it in following document

http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:4554963

unoexperto avatar Feb 16 '16 16:02 unoexperto

@Klortho @jeffbeckncbi Hey guys! How is it going ? :)

unoexperto avatar Dec 13 '17 18:12 unoexperto