Moving from Bookends to Zotero WITH attachments (2019 edition)

iljajj

Hi all,

Because of going from a Mac-only workflow to a mixed Windows/Mac one, I want to move my Bookends library to Zotero. The problem is that the refs transfer without issue, but the connection to attachments (4000+) is lost. I can of course tweak the Bookends export (Endnote XML) but before embarking upon that task I'd like to ask whether any of you had successfully performed it before and if so, how.

Thanks in advance,
Ilja

bwiernik

Do the instructions here regarding placing the xml file in the same location as your attachment storage folder work?
https://www.zotero.org/support/kb/importing_records_from_endnote

If not, can you export one item with an attachment and then copy the XML code here, wrapping it in <code> </code> tags?

iljajj

Hi, thanks for replying - some expert advice would be very welcome. An example:

<record><database name="Research Literature.bdb" path="/Users/ilja/Sync/Research/Bibliographies/Research Literature.bdb">Research Literature.bdb</database><source-app name="Bookends" version="13.2.6">Bookends</source-app><rec-number>5618</rec-number><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" size="100%">Anon</style></author></authors></contributors><titles><title><style face="normal" size="100%">The Diplodocus Carnegiensis</style></title><secondary-title><style face="normal" size="100%">Medical Record. A Weekly Journal of Medicine and Surgery</style></secondary-title></titles><pages><style face="normal" size="100%">543</style></pages><volume><style face="normal" size="100%">63</style></volume><dates><year><style face="normal" size="100%">1903</style></year><pub-dates><date><style face="normal" size="100%">1903</style></date></pub-dates></dates><notes><style face="normal" size="100%">The following values have no corresponding Zotero field:&#xD;auth-address: New York</style></notes><urls><related-urls/><pdf-urls><url><style face="normal" size="100%">file://localhost/Users/ilja/Sync/Publications/Research%20Library/Anon%20-%201903%20-%20The%20Diplodocus%20Carnegiensis.pdf</style></url></pdf-urls></urls></record>

It's obvious I should change the path, but that doesn't generally seem to do the trick. Any other suggestions? There's a lot of injected, but that is presumably either due to Bookends or an earlier migration from Mendeley a few years ago.

Edit: replaced irrelevant example with a more fitting one.

dragonfly

I do not have a Mac (I am on Ubuntu) and I do not use Bookends. But recently I have been studying how to integrate Zotero with other tools in an overall development workflow. A toolchain.

One such tool which might help in migrating your Bookends into Zotero ecosystem is (for Mac users only) Alfred.

https://www.alfredforum.com/topic/8817-bookends-search-and-citations/

In the Ubuntu world I am hooking up a Zotero profile to a similar tool - Alfred - to automate development tasks.
Only recently I found references to Albert and Alfred here.

https://www.rickwest.co.uk/albert-laravel-docs/

I am now using a Zotero collection to hold references to documents from various development sites to create the index to pump into Algolia/Albert.

Possibly Alfred will help in the migration from Mendeley to Zotero. Think toolchain.

Another link here.

https://www.alfredforum.com/topic/10687-bookends-tools-—-a-curated-toolset-for-bookends-reference-manager/

adamsmith

@iljajj -- the problem is that while this has the path to the bookends database, it doesn't mark a file attachment at all, not even a filename -- I don't see how Zotero would be able to import files based on that information.

Does bookends still provide support? Can you ask whether/how it's possible to include the filepath or at least the filename in the export?

iljajj

Sorry, my bad. I had stupidly copied in a reference (one of very few) without a PDF attachment. This is more relevant:

<record><database name="Research Literature.bdb" path="/Users/ilja/Sync/Research/Bibliographies/Research Literature.bdb">Research Literature.bdb</database><source-app name="Bookends" version="13.2.6">Bookends</source-app><rec-number>5618</rec-number><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" size="100%">Anon</style></author></authors></contributors><titles><title><style face="normal" size="100%">The Diplodocus Carnegiensis</style></title><secondary-title><style face="normal" size="100%">Medical Record. A Weekly Journal of Medicine and Surgery</style></secondary-title></titles><pages><style face="normal" size="100%">543</style></pages><volume><style face="normal" size="100%">63</style></volume><dates><year><style face="normal" size="100%">1903</style></year><pub-dates><date><style face="normal" size="100%">1903</style></date></pub-dates></dates><notes><style face="normal" size="100%">The following values have no corresponding Zotero field:&#xD;auth-address: New York</style></notes><urls><related-urls/><pdf-urls><url><style face="normal" size="100%">file://localhost/Users/ilja/Sync/Publications/Research%20Library/Anon%20-%201903%20-%20The%20Diplodocus%20Carnegiensis.pdf</style></url></pdf-urls></urls></record>

I've updated the older example as well.

adamsmith

OK, that looks like it'd definitely be possible; let me investigage -- I'd be curious, though, if this works to import PDFs if you just remove the localhost, i.e.
file:///Users/ilja/... etc.

iljajj

I tried that, but with mixed results. It seems that diacritics may present a problem, and there's a lot of umlauts in there. But I wouldn't know where to look for a solution...

adamsmith

Mixed results would mean that the filepath works, though, so that part is solved. Could you post an example with diacritics then? Zotero expects and would import utf8, but if Bookends exports something else, that's probably fixable.

iljajj

Thanks such a lot for thinking along. Have a gander at this one:

<record><database name="Research Literature.bdb" path="/Users/ilja/Sync/Research/Bibliographies/Research Literature.bdb">Research Literature.bdb</database><source-app name="Bookends" version="13.2.6">Bookends</source-app><rec-number>32344</rec-number><ref-type name="Journal Article">17</ref-type><contributors><authors><author><style face="normal" size="100%">Böhme, Gottfried</style></author></authors></contributors><titles><title><style face="normal" size="100%">Otto Jaekel und das Museum für Naturkunde der Berliner Universität</style></title><secondary-title><style face="normal" size="100%">Wissenschaftliche Zeits chrift der Ernst-Moritz-Arndt-Universität Greifswald, Mathematisch-naturwissenschaftliche Reihe</style></secondary-title><short-title><style face="normal" size="100%">Otto Jaekel und das Museum</style></short-title></titles><pages><style face="normal" size="100%">18-21</style></pages><number><style face="normal" size="100%">1-2</style></number><volume><style face="normal" size="100%">38</style></volume><dates><year><style face="normal" size="100%">1989</style></year><pub-dates><date><style face="normal" size="100%">1989</style></date></pub-dates></dates><keywords><keyword><style face="normal" size="100%">History of Science</style></keyword><keyword><style face="normal" size="100%">Berlin</style></keyword><keyword><style face="normal" size="100%">Museum für Naturkunde</style></keyword><keyword><style face="normal" size="100%">Jaekel, Otto Max Johannes</style></keyword></keywords><notes><style face="normal" size="100%">Wissenschaftliche Zeitschrift der Ernst-Moritz-Arndt-Universität Greifswald, Mathematisch-naturwissenschaftliche Reihe&#xD;&#xD;http://stabikat.de//DB=1/LNG=DU/CLK?IKT=12&amp;TRM=129306851</style></notes><urls><related-urls/><pdf-urls><url><style face="normal" size="100%">file://localhost/Users/ilja/Sync/Publications/Research%20Library/Bo%CC%88hme%20-%201989%20-%20Otto%20Jaekel%20und%20das%20Museum%20fu%CC%88r%20Naturkunde%20der%20Berl.pdf</style></url></pdf-urls></urls></record>

adamsmith

OK, so Bookends URL encodes the umlauts in filepaths -- seems like an odd choice to me, but maybe they have a reason. I think I should be able to put up a (custom) version of the import translator that fixes that for you on import tonight.

adamsmith

Download the translator from here: https://gist.githubusercontent.com/adam3smith/dcbb93ac423d3d37428b154245d9e38c/raw/af2026bd2524e99a8f3c2e3d05f4822dee6859d8/bookends-endnote.xml (right-click --> save link as) and save it to the translator forlder in your Zotero data directory. https://www.zotero.org/support/zotero_data
Completely restart Zotero, then try import again -- should work now (the translator also automatically removes the localhost part of the filepath).

iljajj

It's chugging along right now, but everything seems to go fine. Thank you SO much for devoting attention to my issue - this is going a long way to finally getting me to a full Zotero workflow.

Would you mind if I were to share your link on the Bookends forum, as I know others have been grappling with this as well?

adamsmith

Yes of course feel free to share. FWIW, you can remove the translator from Zotero simply by deleting the file, though the only thing it affects is import of Endnote XML files, so it's not important to delete it.