PDF not automatically downloading

mboivin

Hi everyone,

I have been Zotero uster for a long time and since the upgrade to 3.0 the PDF saving has been a bit strange. When Zotero saves it is not keeping a copy of the PDF but is actually taking 2 snapshots of the webpage.

It is just strange. I have been just manually saving them and linking them to the citation but it screws up my syncing with the server as I wont be able to access them on my secondary computer.

I am currently using Firefox 10.0.1 and Zotero 3.0.2

Any suggestions would be greatly appreciated

Mike

adamsmith

sample URLs? I doubt this is the case for all sites.

edit: also, you can manually attach a pdf ("attach stored copy of file" or just drag it to Zotero) in a way that will sync.

mboivin

Thanks for the quick reply Adam.

It has been happening through the corporate article websites such as Ingenta, Sage, and pubmed central

Example of article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779173/

Could it be an issue through the proxy settings for my university?

You are right I have been just manually attaching the PDF and it works perfectly fine but I just miss the automatic download feature.

Thanks for your help,

Mike

adamsmith

that's odd. That pdf attaches fine for me.
You made sure that you still have the "automatically attach pdf" option checked in the general tab of the Zotero preferences, correct?
Try disabling all other Firefox preferences to make sure that's not interfering, restart FF and try again.
You could also temporarily disable proxy re-direction in the proxy tab of the Zotero preferences. We usually need this to get pdfs from commercial databases, but it's not necessary for PubMed and if something isn't working right with it, that might mess with the pdf attaching.

mboivin

Thanks Adam,

I double checked on the automatic download. It is funny thing. It works fine with Science direct (Elsevier) but on other sites that it used to work on are not working.

I tried disabling features that I don't use and restarted... no improvement.

I think disabling the proxy settings of my zotero would cause me way more time and grief (the proxy settings is a great feature... I mean GREAT feature).

I am ok doing the manually saving of the PDF's, it really is very little work but I just wanted to make sure I was not missing something very obvious.

Thanks so much Adam for all your help!!!! There are very few bigger fans of Zotero than I am. :)

adamsmith

The proxy disabling isn't going to be permanent - I just want to see if it has an effect.
Same for other add-ons - please try disabling all non-Zotero Firefox add-ons, even the ones you can't live without, for troubleshooting.

mboivin

Adam it is my proxy settings. I disabled... grabbed the PDF no problem. Once activated again, it would not download the PDF.

Any suggestions?

adamsmith

do you see the pubmed URL above proxied? If so, is there any reason pubmed needs the proxy?
Else it would be possible to manually remove proxy redirection for pubmed only.
Also, would you mind posting a full proxied URL so we can see the structure of your proxy? If you're really concerned, you can xxx out your institution, but there is really no reason.

mboivin

Thanks Adam,

Here is the full proxy URL:

http://www.ncbi.nlm.nih.gov.myaccess.library.utoronto.ca/pmc/articles/PMC2779173/

I removed the proxy for the ncbi.nlm in my proxy settings and it works. So for open access resources I will remove the proxy settings to get around the problem.

adamsmith

Great - I can replicate not getting the PDF from pubmed when it's proxied so that's not a problem with your particular proxy.
The problem is that Zotero doesn't recognize pubmed anymore when it's proxied (hove over the translator and you'll see "Embedded Metadata" when it's proxied, but "PubMed Central" when it's not.)
I'll see if this is a translator-specific issue or a more generic issue.

If you come across other examples from other databases that'd be helpful.

mboivin

Adam I am currently reseaching 3 other large projects. Do you want me to post any databases in this forum or would you like for me to send them to you directly?

Happy to help and support any way that I can.

Mike

adamsmith

please post here - if this is a general issue we'll have to call in the big guns ;-).

mboivin

Hi Adam,

The following link through the proxy lead to 2 snapshots of the reference being taken but no pdf.

http://www.annals.org.myaccess.library.utoronto.ca/content/148/2/141.full

I hope this helps,

Mike

Simon

Have you tried with Zotero 3.0.3, which came out last night?

mboivin

Thanks so much Simon,

It worked beautifully!!!

Greatly appreciate your help and support,

Mike

sorex

Hi,
I've found this thread while searching the forum for my case : Zotero (3.0.3 FF 10, windows Xp or 7) does not attach pdf files neither snapshots when importing from Pubmed or Wos. Both Join pdf and snapshot options are checked. BTW pdf are attached through the corporate websites (as Elsevier, Nature, etc) with proxy option enabled.
I tried to disable one by one several options (proxy, openURL, pdf/snapshot checkboxes), then to enable one by one restarting each time.
The issue in this thread seems to be solved with 3.0.3 - it's not my case...
Can anyone help please?

Simon

sorex: Neither PubMed nor Web of Science provide PDFs. Zotero can only download PDFs from databases that provide them, which usually means journal websites.

Closing this thread, because, while there are probably more PDF-related issues to be found, the one described here is fixed.