problems with DOI & Extra fields

hello, i'm a satisfied zotero user.
Today i realized that has happended two bad things to my library:

1) on 139 items in my library, in almost all items the PMID & PMCID numbers stored in the extra field has disappeared (they are disappeared also into my online library and from exported RDFs too). it's a known behavior?

A zotero word plugin bug seems that partially saved me from this situation: i have all my library cited into a word document. many times a day i click on the refresh button in word (the "update all citation to reflect changes" function). Although all my extras has now gone, if i click just now on the refresh button, zotero word plugin doesn' reflect this change, so all my PMID&PMCID numbers are still stored into my word document. So i can manually copy&paste all of them into my zotero library.

this zotero word plugin refresh bug doesn't happens if just now i create a new document with new bibliography: citations added has the extra field gone.


2) DOI field has disappeared from all books and book chapters in my libary. I realized this because I found them (DOIs of books and book chapters only) stored in the abstract field. why this behaviour? screenshot: https://imgur.com/a/oxL7E

also in this case the zotero word plugin refresh button doesn't have effect, so citaton in my word document appears still appears with the DOI. screenshot:
https://imgur.com/a/RPgHI

and, also in this case, this zotero word plugin refresh bug doesn't happens if just now i create a new document with new bibliography: citations added without the DOI (and abstract isn't covered into the citation style used).



Thinking about it, the only "odd" thing I did was a few days ago, which I downgraded from the (lastest) beta version of zotero to the (lastest) stable version (because i switched over an year ago from stable to beta in order to use some beta features that now are embedded in the stable version, so i switched again to stable branch). does it have anything to do with it?

There is a better method (than manual copy&paste from word document to my library) for recover all my extra pmid&pmcid?
There is also a method for recover the DOI field in books and book chapters?

thanks for the help.
  • Did you do anything to restore data? Export/import or so?

    The fact that items don't update in Word suggests thes are different items in your library, not the same ones with DOI/PMID removed.
  • hello and thanks for your quick responce.
    yes, some days ago i made an export of my library, and later i imported the just exported rdf file. then i check if my zotero online library was corrected sync and "seems" there wasn't problems (but obviously I did not mind the doi and extra fields ..).
    why importing a just exported rdf could cause the loss of extra field content? and about the lost of the DOI field, whats happended? thanks for your support
  • I'm not sure about the details, but Zotero RDF isn't 100% faithful on import/export, so that seems pretty likely to be the cause -- especially since we're talking workarounds in the extra field. Why did you do export/import? That actually messes with a whole range of things (sync, Word documents, for example).

    Do you happen to have a copy of your Zotero data folder from before that?
    https://www.zotero.org/support/zotero_data
  • my rdf backups are too recents, so they too are compromised, and i don't have older backups with still present the correct extra informations. i never used to copy my zotero user folder, because i believed that the import-export was a secure machanism for backup.

    if the rdf format isn't 100% perfect in import/export, what is the best file format for this purpouse?

    some days ago i did the export (like every day, for backup), then I accidentally edit my library in a wrong way (nothing to do with the extra field), so i did the import for restore the library to a correct state. and problably this compromised my extra fields...

    about z word plugin:
    I believed that every item had an unique number so an import/export would not have affected the z word plugin behavior. but I'm understanding that an import compromises the links between library items and document in which they are cited, is it correct?
    and copying the user folder (instead of import/export) compromises at the same manner?

    thanks
  • I believed that every item had an unique number so an import/export would not have affected the z word plugin behavior. but I'm understanding that an import compromises the links between library items and document in which they are cited, is it correct?
    and copying the user folder (instead of import/export) compromises at the same manner?
    The part about the unique IDs is correct, but they are not part of export, which is why export/import breaks the link to Word documents. Copying your data folder, on the other hand, keeps your database intact as is, which is why that's the recommended way to back-up:
    https://www.zotero.org/support/zotero_data#backing_up_your_zotero_library
    I think you're probably best off to identify and re-populate the information gone missing and then use recommended back-ups from now on forward.
  • thanks for the explanation. I suggest to make appears a message window when the user use the import/export function; a window that inform to you that is not a valid backup method (with the button for hiding the message the next times).

    i found an old zotero.sqlite.bak. so, in which manner i can only look the content of this file (without import nothing into my library) and do manual copy&paste of extra fields?

    thanks.
  • Looking at the sqlite file is a mess -- wouldn't it make more sense to restore from that and the add the missing items from the last exported Zotero RDF?
  • i made a lot of important edits from this old backup to now.
    there is a chance to run my zotero installation togheter with an "isolated" (like portable) version of zotero, then use it for open the old sqlite backup and make copy&paste to my right zotero installation?
Sign In or Register to comment.