Migrating from Papers3 to Zotero: no pdfs appearing

Hello

I'm transferring my library from Papers3 to Zotero. I've tried the transfer as .xml, .bib and .ris libraries. All 3 work well (the .bib and .ris seemed cleaner than the .xml, all 3 captured my tags and notes). However, whichever method I use, none of the PDFs attached to the entries in Papers (which are stored in Dropbox) are transferring into Zotero. Any ideas?

I couldn't find the answer in the previous posts from other Papers3 refugees, only people who'd had the opposite problem of duplicate imports.

I see when I export from Papers, the options in the Export menu are

"Bibtex Library
Endnote XML Library
Refman RIS File
___
PDF Files and Media
Reference List
Notes
___
Papers Archive"

(I did a test export of a PDF and then imported it into Zotero, and was pleased to see it preserved the highlights and got the metadata. Importing the pdf directly from the Dropbox folder that Papers uses also worked, but without the highlights. But either way I wouldn't need to do the PDFs separately to the library?)

I must be missing something but not sure what

Thanks in advance

Nikki
  • Bump - any help much appreciated
  • Using zotero Beta if that changes anything
  • Can you open the RIS and Endnote XML file and see if/how the PDF files are listed there?
  • Ah I should have thought of that. It looks like the links to the pdfs are in the RIS and XML files, but aren't importing (despite ticking that option on the import settings).

    A typical entry in the RIS file looks like this with the file path to the PDF near the bottom:

    TY - JOUR
    ID - 65EB02D2-E5E3-43CA-925F-C5E43B8D42E8
    T1 - Optimization of competitor poly(dI-dC) poly(dI-dC) levels is advised in DNA-protein interaction studies involving enriched nuclear proteins
    A1 - Larouche, K
    A1 - Bergeron, M J
    A1 - Leclerc, S
    A1 - Guerin, S L
    Y1 - 1996/03/01
    N1 - EMSA dI-dC concetration paper saying that can also abolish specific binidng even at low concentrations
    N2 - Procedures used for investigating DNA-protein interactions, such as the electrophoretic mobility shift assay (EMSA) or DNasel footprinting, require that exogenous nucleic acids (or synthetic equivalents) be added to the reaction mixture to prevent or reduce the nonspecific interaction of nuclear proteins with the labeled probe of choice, especially when proteins are obtained from crude nuclear extracts. One of the most potent, and likely the most widely used, non-specific competitor is the synthetic polymer poly(dI-dC).poly(dI-dC). Its addition to the reaction mixture prior to crude nuclear proteins has unquestionably proven very efficient in reducing nonspecific interactions by facilitating detection of the complexes of interest. However, in certain instances, the use of crude extracts alone does not provide adequate answers and the need to further enrich such extracts becomes absolutely necessary. In this study, we provide evidence that amounts of poly(dI-dC).poly(dI-dC) well below those currently described in the literature substantially impair, or even totally prevent, the detection of specific DNA-protein complexes in EMSA when enriched, gel-fractionated or commercially purified nuclear proteins are used, therefore indicating the need to precisely optimize the amount of such a competitor in DNA-protein interaction studies.
    KW - Methodology
    T2 - Biotechniques
    J2 - BioTechniques
    VL - 20
    IS - 3
    SP - 439
    EP - &
    AD - CHUL Research Center, Qu├ębec, Canada.
    UR - http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=8679204&retmode=ref&cmd=prlinks
    L1 - file://localhost/Users/nikkihall/Dropbox/Program%20libraries%20and%20syncing/Library.papers3/Files/06/0690DC3C-EA75-481A-B5FD-99A39216BA16.pdf
    L3 - papers3://publication/doi/10.2144/19962003439
    M3 - 10.2144/19962003439
    ER -

    I can't see a pdf link in the imported entry anywhere. Whereas if I add the link manually (right clicking -> Add Attachment -> Add link to file) then it appears easily.

    Hope that helps
  • Can you try removing localhost/ so that the part after L1 - reads:
    file:///Users/nikkihall/Dropbox/Program%20libraries%20and%20syncing/Library.papers3/Files/06/0690DC3C-EA75-481A-B5FD-99A39216BA16.pdf

    Just test with that single entry in a new file. If that works, we can look at updating import to filter that out, but it's obviously also an easy find&replace on your part.
  • Thanks so much for your help. I've got it to work now.

    It wasn't localhost/ that was the problem, but it was indeed the pdf file path, thanks for pointing me in the right direction.

    The export and hence file path was generated on a different MacBook to the one I am importing on (Papers3 crashes on my newest computer despite still running OSX Catalina). I checked the file path via 'Get Info' and saw that on the current Mac it is not Users/nikkihall but a slightly different account name. All sorted.
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