automated PDF retrieve via DOI in metadata

ZeZeHuang
Hi,

I accidentally delete all my storage PDF files : (
Though, I have synced all my references to my zotero library (refs only without PDF files). Luckily, when I logged in and synced, they are all there. So what I would like to ask is:

Is there a way to ask Zotero to retrieve PDFs from the DOI in metadata of each item?

I have tried to use the newly released function "find available PDFs" of Zotero, though only partial PDFs were obtained (30/3xxx refs). it seems to be the same case when I am in edu domain, so the paywall should not be the cause of this problem. I assume the Zotero PDF finding function doesn't work via DOI or URL in metadata, because almost all my items have those in the metadata.

Thank you guys in advance

  • bwiernik
    Retrieve PDF does use DOI or URL (in fact that is all it uses)—have you checked that you actually have access to a PDF if you follow the DOI link manually? If so, can you give an example of a DOI that doesn’t find a PDF?
  • ZeZeHuang
    @bwiernik Yes, these DOI are functioning that may take me to the PDF using my browser. Though, I found my question is that PDFs are not downloaded locally. I am thinking to use Zotfile to sync to my Dropbox.

    I attached a screenshot of my current situation: https://www.dropbox.com/s/qzeyl1r62h9s85r/123.jpg.png?dl=0

    Thank you!
  • dstillman
    edited April 22, 2019
    If you're saying that "Find Available PDF" doesn't download a PDF, we'd want to see a Debug ID for that happening. Note that that function currently can only download files that you have direct or VPN-based access to, so your being able to access the PDFs when you open the URL in your browser via a web-based proxy wouldn't be relevant. You need to be able to access them with non-proxied URLs and without logging into anything in your browser.
  • ZeZeHuang
    @dstillman here is the Debug ID: D1933741270. Yes, that's what I mean, I only can access those links while I am VPN to my edu domain. I am looking for a solution to download these files locally where I can open without logging into anything.

    Thanks!
  • dstillman
    See the instructions again. That's just debug output for Zotero startup, not for this action.
  • ZeZeHuang
    @dstillman
    I followed the Debug ID instruction generating ID and debug logs. Not sure is that what you need:
    (2)(+0000024): Attachment file '/home/xxxxx/Dropbox/Zotero backup/Wong et al. - 2019 - The Influence of Contrasting Microbial Lifestyles .pdf' not found
    (2)(+0000002): Attachment file '/home/xxxxxx/Zotero/storage/LTGHQHCB/Truong et al_Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along.pdf' not found

    Thank you!

  • dstillman
    We need the Debug ID for actually performing the "Find Available PDF" action that you're reporting a problem with, not trying to open a file.
  • ZeZeHuang
    Interesting, that's what I did. Though I don't see this action was recorded.
    Here is what I did:
    1. selected items
    2. right click
    3. select "Find Available PDFs"
    4. a window pop up in the right bottom showing "Find Available PDFs No PDFs found"

    I did the abovementioned actions with logging enabled as instructed in the page. I did't try to open a file.
  • dstillman
    Can you try again?
  • dstillman
    (And the debug output you provided is from Zotero startup, which isn't necessary here.)
  • ZeZeHuang
    edited April 22, 2019
    I see, sorry for posting that here.

    Yes, I tried it again and the "Find Available PDFs" action is not recorded, so I don't have a ID to report. Any suggestion?
  • dstillman
    Oh, you're trying "Find Available PDFs" on multiple items, not "Find Available PDF" on a single item. Zotero won't look for PDFs for items that already have PDFs attached. It won't show the "Find Available PDF" option for single items where it doesn't apply, but if you select multiple items it will always show it as an option.

    If you want to use "Find Available PDFs" you'll need to delete the attachment items with missing files first.
  • ZeZeHuang
    Oh, I see. That makes sense! Then my next question would be: how can I delete the attachments in batch? I don't see them in my local drive, neither in other sync folders.

    Thanks
  • dstillman
    You can create an advanced search for [Attachment File Type] [is] [PDF] and [Attachment Content] [does not contain] [ ] (space), save it as a saved search, and then do a Select All (Ctrl-A) in the list to select only the matches and delete them.

    The "Attachment Content" condition may not be 100% accurate, so you'd want to verify that the blue dots in the right-hand column were all empty to make sure you weren't deleting any attachments that actually had files attached.
  • ZeZeHuang
    I tried and it worked (most of them were deleted)!! Thanks. And I can retrieve files from the PDF finding function. Thank you!
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