Searching PubMed broken 2/15/2012

[Jon]

NCBI made some changes in the way they return the results of a PubMed search, which broke the Bookends PubMed parser. We've made the changes needed to deal with this and will be uploading a new version of Bookends tonight.

Although PubMed searches in Bookends 10.x will not work, searching via Bookends Browser (Online Search window) should still be OK.

Jon
Sonny Software

[Jon]

Bookends 11.2.6 is now available on our web site, and should restore PubMed search (and add a few other new things).

ADDED 2/20/12: It's also available now on the Mac App Store.

Jon
Sonny Software

[pavitra]

And there's no patch for 10.x if we don't have the upgrade?

[Jon]

No, version 10.x is not under development.

You can still import from PubMed with 10.x however. Use your browser (or Bookends browser) to search PubMed. Tell PubMed to display the references you want in MEDLINE format. Copy to the clipboard and, in Bookends, import from the clipboard using the PubMed filter.

Jon
Sonny Software

[dspedersen]

Jon, there might be problems with pubmed again. Can't seem to get searching going. Only thing that's returned is either There are no matches or PMID- Supplied id parameter is empty.PMID: every second time. I've tried the same search terms successfully directly on pubmed.

Best,
Dan

[Jon]

It's working now. Don't confuse periodic problems with the PubMed server going down (happens too often for my taste, and there's nothing Bookends can do about it) and fundamental changes in PubMed that break Bookends. If something is intermittent, it's the former (and that seems to be the case here).

Jon
Sonny Software

[dspedersen]

Sorry about that. However, the search worked fine on their site; thus I thought it might be a "communication" problem relating to possible changes at pubmed's end.

Best,
Dan

[Jon]

The server for the PubMed web site and the server used to directly search PubMed via their APIs are separate, and it's not uncommon for one to go down while the other continues to function. As I said, if they make a change that breaks the Bookends parser, that's permanent and requires our intervention. If it's an intermittent problem (doesn't work now, works in 30 minutes, then doesn't work again, etc.) it's a temporary problem on their end.

Jon
Sonny Software

[dspedersen]

I understand that, though I do not understand why PubMed search in Papers2 is working (they are using the same APIs, right?), while that of BE does not. Have the same problem again; at least BE finds the necessary info when dragging a PDF into BE. Reckon I must patiently wait for PubMed to work normally again.

Best,
Dan

[Jon]

This is a new issue (as of 6/19/12). PubMed is now acting bizarrely when we use the cookie they sent Bookends when the query was first made. I've filed a request with NCBI that they fix this. If they don't do that soon, we'll release an update that works around the problem. BTW, can still use Bookends Browser to search PubMed, too, and get the references and pdfs.

Jon
Sonny Software

[dspedersen]

The problem seems to be persistent; I still get "PMID- Supplied id parameter is empty.PMID:" and even drag'n'drop of PDFs seems to be broken:

[Jon]

You can be certain that we're aware of this. They've had one day to fix this. We'll be releasing an update Saturday if it's not done by then. In the meantime, you can use Bookends Browser to search PubMed and import references and pdfs.

Jon
Sonny Software

[Jon]

Since NCBI hasn't responded, we'll be releasing 11.3 early tomorrow morning (Saturday). The Mac App Store version will follow when Apple has reviewed it.

We had planned to have some substantial additions in 11.3, but we'll hold off on them since we have to release 11.3 early to deal with the PubMed problem. I'll note, however, that 11.3 has some hidden new features that will become apparent when other software companies with whom we are partnering release new versions of their popular apps. Just a teaser.

Jon
Sonny Software

[dspedersen]

Jon, that is super great news! It was beginning to get a bit cumbersome to reference mine and download via the built-in browser (even though I discovered a few things ).

Btw, I can't seem to get the download working; nothing happens when clicking this:



Oddly, the other buttons work just fine.

hidden new features that will become apparent when other software companies with whom we are partnering release new versions of their popular apps. Just a teaser.

Uh! Almost like Christmas time

[Jon]

That HUD is actually imposed by WebKit, bypassing our own code (i.e. we don't control it). We do provide many ways to download pdfs. If you tell me from where you were trying to download it (e.g. Bookends Browser) I can tell you how to do it.

Jon
Sonny Software