Bookends pauses while exporting xml -- anyone else?

thecritic · Post by **thecritic** » Thu Oct 04, 2007 2:19 am

I keep experiencing a problem in Bookends 10 where the program will pause during an export (EndNote xml) of a large number of references; I have to keep moving my mouse to get the export to continue.

When I informed Jon about this, he wrote that something was wrong with my computer, but the problem does not occur with 9.2.2 or any other program, for that matter.

I have a PowerBook G4/1.67 Ghz (i.e. PPC) with 2 GB of RAM running OS X 10.4.10.

Could someone with a similar configuration try shift-clicking the "marked" checkboxes in their library to mark all, choose "Export References(hits)," then Export Hits as xml (EndNote 8 or later) and post their results here?

Jack Post · Post by **Jack Post** » Thu Oct 04, 2007 4:03 am

I have exactly the same configuration. And I have the same behavior of BE during the export of XML: the program pauses and the CPU use drops to zero.
I had to click for a long time and since I shift-clicked the mark boxes, I had to export all references since the stop button didn't work as well.

Jack

thecritic · Post by **thecritic** » Thu Oct 04, 2007 4:50 am

Jack Post wrote:I have exactly the same configuration. And I have the same behavior of BE during the export of XML: the program pauses and the CPU use drops to zero.
I had to click for a long time and since I shift-clicked the mark boxes, I had to export all references since the stop button didn't work as well.

Thanks. Jon, do you have any idea what the problem might be?

happymac · Post by **happymac** » Mon Oct 08, 2007 1:56 am

thecritic wrote:I keep experiencing a problem in Bookends 10 where the program will pause during an export (EndNote xml) of a large number of references; I have to keep moving my mouse to get the export to continue.

I just tried this, and it also happens on my PowerBook G4/1.33 GHz. Is this a problem with my machine, or does it lie somewhere else?

Post by **Jon** » Mon Oct 08, 2007 8:36 am

happymac, I can't reproduce this on two machines (PPC and Intel). But I'm working with someone who can, so if I can figure out why it behaves this way on some systems I'll take care of it.

Jon
Sonny Software

happymac · Post by **happymac** » Mon Oct 08, 2007 4:39 pm

Jon wrote:happymac, I can't reproduce this on two machines (PPC and Intel). But I'm working with someone who can, so if I can figure out why it behaves this way on some systems I'll take care of it.

Thanks, Jon. Wow, I really appreciate the quick response!

I have another question for you about EndNote xml export. After many unpleasant experiences in the past, I made a promise to myself always to make sure that I can easily export the data from any program that I settle on. I performed some tests, and when I export references from Bookends back to EndNote, the attachment links don't transfer even though the URL is visible in the EndNote reference. Do you know what could be wrong?

Post by **Jon** » Mon Oct 08, 2007 4:55 pm

Hi,

I think the EN XML export lag is fixed in the next beta. We'll see.

EN keeps its attachments in specific folders (which ones, I believe, vary between versions of EN). But the pdfs are kept in folder that have the pdf name plus an ID that EN supplies. I don't see anyway of creating that outside of EN. Perhaps someone else more familiar with EN has an idea, but at the moment I think you'd have to actually reattach in EN...

Jon
Sonny Software

happymac · Post by **happymac** » Mon Oct 08, 2007 5:28 pm

Jon wrote:I think the EN XML export lag is fixed in the next beta. We'll see.

Wow, great. Thanks so much.

Jon wrote:EN keeps its attachments in specific folders (which ones, I believe, vary between versions of EN). But the pdfs are kept in folder that have the pdf name plus an ID that EN supplies. I don't see anyway of creating that outside of EN. Perhaps someone else more familiar with EN has an idea, but at the moment I think you'd have to actually reattach in EN...

I took a look at exported xml from EndNote... It's goobledygook to me, but I see stuff like this:

<urls><pdf-urls><url><style face="normal" font="default" size="100%">file://localhost/Users/happymac,filename.pdf</style></url></pdf-urls></urls>

I don't see a tag <pdf-urls> in the Bookends xml. Could that be it?

Post by **Jon** » Mon Oct 08, 2007 7:45 pm

I'm not sure what version of EN you are looking at. In X, the pdf name has a number id tag, like "AbrÃ¡ham et al 2001-0741789696" followed by the file name: "/AbrÃ¡ham et al 2001.pdf". The long number at the end is added by EN.

Jon
Sonny Software

happymac · Post by **happymac** » Tue Oct 09, 2007 12:37 am

Jon wrote:I'm not sure what version of EN you are looking at. In X, the pdf name has a number id tag, like "AbrÃ¡ham et al 2001-0741789696" followed by the file name: "/AbrÃ¡ham et al 2001.pdf". The long number at the end is added by EN.

I'm referring to EndNote X as well. I think that EndNote can be used in two ways. According to the manual, p.396:

"You can specify an absolute path to a specific folder, or you can specify a relative path to copy the PDF file to your libraryâ€™s .DATA\PDF folder. "

In addition, p.236:

"When you insert a link to a file with the PDFLink to PDF command from the References menu, the file dialog includes a check box titled, "Copy this file to the default PDF folder and create a relative link."

When I drag pdfs from whatever folder I want to the EndNote library window, it is added to the library and not renamed in any way (I'm not given a choice to let the program manage attachments -- another area in which Bookends is better). I think that the "relative path" option is somewhat like Bookends' use of a single attachments folder -- libraries become self-contained.

So is what you're talking about the "relative link" case? If you don't use relative links, then I think that the file names and links are preserved.

But in the case of *export* from Bookends, the relative links to the library's .DATA\PDF folder don't apply, do they? So do you think it would be possible upon export to preserve links, even to a single attachments folder?

Post by **Jon** » Tue Oct 09, 2007 7:12 am

Bookends could output the absolute link. I can try that and see if EN accepts it. Thanks for the followup.

Jon
Sonny Software

happymac · Post by **happymac** » Tue Oct 09, 2007 8:24 am

Jon wrote:Bookends could output the absolute link. I can try that and see if EN accepts it.

It should work, but you might also have to use that different <pdf-url> tag. See http://www.endnote.com/support/ensupport.asp for the "xml dtd" document.

Thanks so much for being willing to revisit this!

happymac · Post by **happymac** » Wed Oct 10, 2007 2:31 am

Jon wrote:I think the EN XML export lag is fixed in the next beta.

It is fixed. Wow. Thanks. You haven't had a chance to work on attachment URL export in the 10.1 beta yet, have you? My attachments are still lost upon export from beta 2. (not to worry -- I don't mean to nag -- I just wanted to let you know)

Post by **Jon** » Wed Oct 10, 2007 7:02 am

Glad it's fixed. No, I haven't gotten around to looking at XML export yet.

Jon
Sonny Software

Post by **Jon** » Wed Oct 10, 2007 3:52 pm

OK, I've added full pathnames to attachments in XML exports, and it works so far (in my limited testing) with EN 9-11(EN 8 doesn't recognize this, but that's because EN8 had even more limited support for pdfs). I'll be uploading a beta 3 before long, so please try this with your large database to give it a thorough test.

Jon
Sonny Software

Sonny Software

Bookends pauses while exporting xml -- anyone else?

Bookends pauses while exporting xml -- anyone else?

Bookends pauses while exporting xml -- anyone else? Yes

Re: Bookends pauses while exporting xml -- anyone else? Yes

Re: Bookends pauses while exporting xml -- anyone else?