COinS Translator not working for Nature News

sethmg · April 28, 2011

Hi all,
I'm trying to import the following article:

Education: The PhD factory
The world is producing more PhDs than ever before. Is it time to stop?
David Cyranoski , Natasha Gilbert , Heidi Ledford , Anjali Nayar & Mohammed Yahia

http://www.nature.com/news/2011/110420/full/472276a.html

The icon appears in the location bar, and when I click on it the "importing" window appears, but nothing is saved.

The Debug output when I click the icon is below.

Am I doing something wrong, or is the error in zotero's translator?


(4)(+0124132): Translate: Parsing code for COinS

(5)(+0000001): SELECT libraryType FROM libraries WHERE libraryID=?

(5)(+0000001): Binding parameter 1 of type int: 337248

(5)(+0000000): SELECT groupID FROM groups WHERE libraryID=?

(5)(+0000000): Binding parameter 1 of type int: 337248

(5)(+0000000): SELECT G.* FROM groups G WHERE groupID=?

(5)(+0000000): Binding parameter 1 of type int: 30513

(5)(+0000000): SELECT COUNT(*) FROM groups WHERE groupID=?

(5)(+0000000): Binding parameter 1 of type int: 30513

(3)(+0000001): Translate: Beginning translation with COinS

(3)(+0000002):     '0' ...
        'itemType' => "journalArticle"
        'creators' ...
            '0' ...
                'firstName' => "David"
                'lastName' => "Cyranoski"
                'creatorType' => "author"
            '1' ...
                'firstName' => "Natasha"
                'lastName' => "Gilbert"
                'creatorType' => "author"
            '2' ...
                'firstName' => "Heidi"
                'lastName' => "Ledford"
                'creatorType' => "author"
            '3' ...
                'firstName' => "Anjali"
                'lastName' => "Nayar"
                'creatorType' => "author"
            '4' ...
                'firstName' => "Mohammed"
                'lastName' => "Yahia"
                'creatorType' => "author"
        'notes' ...
        'tags' ...
        'seeAlso' ...
        'attachments' ...
        'repository' => "false"
        'DOI' => "10.1038/472276a;"
        'publicationTitle' => "Nature News"
        'ISSN' => "1744-7933"
        'contextObject' => "ctx_ver=Z39.88-2004&rft_id=info:doi/10.1038/472276a;&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nature News&rft.eissn=1744-7933&rft.au=David Cyranoski&rft.au=Natasha Gilbert&rft.au=Heidi Ledford&rft.au=Anjali Nayar&rft.au=Mohammed Yahia"
        'complete' => function(...){...} 


(3)(+0000000): Translate: looking up contextObject

(3)(+0000000): Translate: creating translate instance of type search in sandbox

(3)(+0000000): Translate: Searching for translators for an undisclosed location

(4)(+0000000): Translate: Binding sandbox to http://www.nature.com/news/2011/110420/full/472276a.html

(4)(+0000002): Translate: Parsing code for CrossRef

(4)(+0000003): Translate: Parsing code for Citebase

(4)(+0000002): Translate: Parsing code for NCBI PubMed

(4)(+0000002): Translate: Parsing code for Open WorldCat

(4)(+0000000): Translate: Parsing code for CrossRef

(3)(+0000001): Translate: Beginning translation with CrossRef

(3)(+0000000): HTTP GET http://www.crossref.org/openurl/?pid=zter:zter321&url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rft_id=info:doi/10.1038/472276a;&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nature News&rft.eissn=1744-7933&rft.au=David Cyranoski&rft.au=Natasha Gilbert&rft.au=Heidi Ledford&rft.au=Anjali Nayar&rft.au=Mohammed Yahia&noredirect=true&format=unixref

(3)(+0000187): Translate: Could not find a result using CrossRef: 
0 => doi:10.1038/472276a; not found in CrossRef
url => undefined
downloadAssociatedFiles => true
automaticSnapshots => false

(4)(+0000000): Translate: Binding sandbox to http://www.citebase.org/

(4)(+0000002): Translate: Parsing code for Citebase

(3)(+0000001): Translate: Beginning translation with Citebase

(3)(+0000000): HTTP GET http://www.citebase.org/openurl?url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rft_id=info:doi/10.1038/472276a;&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nature News&rft.eissn=1744-7933&rft.au=David Cyranoski&rft.au=Natasha Gilbert&rft.au=Heidi Ledford&rft.au=Anjali Nayar&rft.au=Mohammed Yahia&svc_id=bibtex

(3)(+0000443): Translate: creating translate instance of type import in sandbox

(4)(+0000000): Translate: Binding sandbox to http://www.citebase.org/

(4)(+0000002): Translate: Parsing code for BibTeX

(3)(+0000012): Translate: Beginning translation with BibTeX

(3)(+0000001): Translate: Translation successful

(3)(+0000000): Translate: Could not find a result using Citebase: 
thrown exception => No error message specified
url => undefined
downloadAssociatedFiles => true
automaticSnapshots => false

(2)(+0000000): Translate: Translation using Citebase failed: 
thrown exception => No error message specified
url => undefined
downloadAssociatedFiles => true
automaticSnapshots => false

(5)(+0000000): Translate: running handler 0 for done

(3)(+0000000): Translate: Translation successful

(5)(+0000000): Translate: running handler 0 for done

(4)(+0004450): Registering observer for [collection,search,share,group,bucket] in notifier with hash Ju'

(5)(+0000000): SELECT itemTypeID AS id, typeName AS name, custom FROM itemTypesCombined WHERE display=2

(5)(+0000001): SELECT itemTypeID AS id, typeName AS name, custom FROM itemTypesCombined WHERE display=1

sethmg · April 28, 2011

By the way, if I copy the doi and paste it into the "Add Item by Identifier" dialogue, it works without a problem.

adamsmith · April 28, 2011

You're doing everything right - I can confirm this.
In addition Zotero throws the error

[JavaScript Error: "No error message specified" {file: "file:///home/sebastian/.mozilla/firefox/yzqr9erm.Zotero%202.1/zotero/translators/Citebase.js" line: 0}]

which would explain why it fails silently (which it never should)

Ajlyon or one of the other translator people would have to take a look - but my understanding of what happens is that the COinS doesn't provide a title (which is set as a minimum condition), so Zotero keeps on looking and the other databases - CrossRef and Citebase - run empty.

adamsmith · April 28, 2011

The problem with the doi is that Zotero doesn't strip the semicolon at the end - because dois do include punctuation, it's very hard to decide what to strip and what not.

sethmg · April 28, 2011

Interesting.

From this document (www.crossref.org/02publishers/doi-guidelines.pdf) it appears that the DOI prefix has no punctuation, so maybe all alpha/symbol characters (except ".") should be stripped ahead of the "/".

Thanks for the quick response.

(edit spelling error)

adamsmith · April 28, 2011

yes, but the problem here (and I'd assume in most cases) is the semicolon at the end the suffix - and for that, the DOI specs say:

Therefore CrossRef limits a DOI to only using the following characters:
"a-z", "A-Z", "0-9" and "-._;()/"

so I don't see how that could be dealt with.

ajlyon · April 28, 2011

Yes, this is pretty clearly a mistake on Nature's side. There's no reason they should be appending the semicolon to the DOI inside the ContextObject-- the ampersand is the delimiter here.

Worth pointing out to them, since they're probably not aware of it and can fix it easily.

adamsmith · April 28, 2011

what's with the silent fail, though - that shouldn't happen, right?

ajlyon · April 28, 2011

That's a common issue with translators-- here the COinS translator keeps trying translators and doesn't do a good job reporting failure when it does fail to find even one that can do the trick. I'll see about getting a proper error message out of it.

ajlyon · April 28, 2011

No, I'm not going to fix the error reporting in the COinS translator at this time. The logic is a little more tortuous than I really want to deal with-- let it suffice for now that the item isn't saved.

ajlyon · April 28, 2011

I've contacted Nature Publishing Group about the underlying DOI issue.